Error unexpected end of input reading http header on https:
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Hoover, David (NIH/CIT) [E]
Dec 11, 2023, 2:41:39 PM12/11/23
to genome...@soe.ucsc.edu
Hi all,
We recently migrated our webserver hosting a local GB mirror from centos7 to rocky8, and now we are seeing a response slowdown for custom tracks. When the custom tracks are loaded, typically we see the error message in the browser window:
Error unexpected end of input reading http header on https://...
The custom track data is stored on a different webserver. I can create the custom tracks on the UCSC site and load them using the remote URL without any problem, so I don't think it is the remote webserver.
Do you know how to debug the problem of slow custom track loading?
David
--
David Hoover, Ph.D.
Computational Biologist
High Performance Computing Services,
Center for Information Technology,
National Institutes of Health
12 South Dr., Rm 2N207
Bethesda, MD 20892, USA
TEL: (+1) 301-435-2986
Email: hoov...@hpc.nih.gov
We recently migrated our webserver hosting a local GB mirror from centos7 to rocky8, and now we are seeing a response slowdown for custom tracks. When the custom tracks are loaded, typically we see the error message in the browser window:
Error unexpected end of input reading http header on https://...
The custom track data is stored on a different webserver. I can create the custom tracks on the UCSC site and load them using the remote URL without any problem, so I don't think it is the remote webserver.
Do you know how to debug the problem of slow custom track loading?
David
--
David Hoover, Ph.D.
Computational Biologist
High Performance Computing Services,
Center for Information Technology,
National Institutes of Health
12 South Dr., Rm 2N207
Bethesda, MD 20892, USA
TEL: (+1) 301-435-2986
Email: hoov...@hpc.nih.gov
Jairo Navarro Gonzalez
Dec 11, 2023, 7:54:34 PM12/11/23
to Hoover, David (NIH/CIT) [E], genome...@soe.ucsc.edu
Hello,
Thank you for using the UCSC Genome Browser and sending your inquiry.
We believe a server configuration issue on your remote server caused the issue. We require the fileserver with your custom track data to accept byte-range requests to visualize it on the Genome Browser. To confirm, could you send us the output for the "curl" UNIX command for one of your bigDataUrls:
Our code expects every line of the HTTP header to end with "\r\n" or "\n". It expects a final blank line ("\r\n" or "\n" only) to terminate the header. If it gets end-of-input before the final "\n" it produces your error.
If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Jairo Navarro
UCSC Genome Browser
--
---
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Hoover, David (NIH/CIT) [E]
Dec 12, 2023, 12:44:53 PM12/12/23
to Jairo Navarro Gonzalez, genome...@soe.ucsc.edu
Hi Jairo,
Thanks for replying so quickly.
I've attached a zip of the curl output `curl -I https://hpc.nih.gov/~maheshg2/MS381_sorted.bam_bigwigfile.bw`.
Like I said, if I create the custom tracks on the Genome Browser hosted at UCSC, rather than our local mirror, I do not see any errors. In this case, both the UCSC and local GB are using the same bigDataUrls for the tracks. If the problem were with the content of the custom track data, or with the output of the byte-range request, I would have expected errors from both our local mirror as well as from UCSC.
David
On 12/11/2023 7:54 PM, Jairo Navarro Gonzalez wrote:
> Hello,
>
> Thank you for using the UCSC Genome Browser and sending your inquiry.
>
> We believe a server configuration issue on your remote server caused the issue. We require the fileserver with your custom track data to accept byte-range requests to visualize it on the Genome Browser. To confirm, could you send us the output for the "curl" UNIX command for one of your bigDataUrls:
>
> curl -I <URL_to_your_file>
>
> Our code expects every line of the HTTP header to end with "\r\n" or "\n". It expects a final blank line ("\r\n" or "\n" only) to terminate the header. If it gets end-of-input before the final "\n" it produces your error.
>
> If you have any further questions, please reply to gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>.
> To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/0b5fd578-6174-f7bc-aa9f-63976a4f489a%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/0b5fd578-6174-f7bc-aa9f-63976a4f489a%40hpc.nih.gov>.
Thanks for replying so quickly.
I've attached a zip of the curl output `curl -I https://hpc.nih.gov/~maheshg2/MS381_sorted.bam_bigwigfile.bw`.
Like I said, if I create the custom tracks on the Genome Browser hosted at UCSC, rather than our local mirror, I do not see any errors. In this case, both the UCSC and local GB are using the same bigDataUrls for the tracks. If the problem were with the content of the custom track data, or with the output of the byte-range request, I would have expected errors from both our local mirror as well as from UCSC.
David
On 12/11/2023 7:54 PM, Jairo Navarro Gonzalez wrote:
> Hello,
>
> Thank you for using the UCSC Genome Browser and sending your inquiry.
>
> We believe a server configuration issue on your remote server caused the issue. We require the fileserver with your custom track data to accept byte-range requests to visualize it on the Genome Browser. To confirm, could you send us the output for the "curl" UNIX command for one of your bigDataUrls:
>
> curl -I <URL_to_your_file>
>
> Our code expects every line of the HTTP header to end with "\r\n" or "\n". It expects a final blank line ("\r\n" or "\n" only) to terminate the header. If it gets end-of-input before the final "\n" it produces your error.
>
> All messages sent to that address are archived on a publicly accessible Google Groups forum.
> If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>.
>
> Jairo Navarro
> UCSC Genome Browser
>
>
> On Mon, Dec 11, 2023 at 11:41 AM 'Hoover, David (NIH/CIT) [E]' via UCSC Genome Browser Mirror-Specific Support <genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu>> wrote:
>
> Hi all,
>
> We recently migrated our webserver hosting a local GB mirror from centos7 to rocky8, and now we are seeing a response slowdown for custom tracks. When the custom tracks are loaded, typically we see the error message in the browser window:
>
> Error unexpected end of input reading http header on https://...
>
> The custom track data is stored on a different webserver. I can create the custom tracks on the UCSC site and load them using the remote URL without any problem, so I don't think it is the remote webserver.
>
> Do you know how to debug the problem of slow custom track loading?
>
> David
> --
> David Hoover, Ph.D.
> Computational Biologist
> High Performance Computing Services,
> Center for Information Technology,
> National Institutes of Health
> 12 South Dr., Rm 2N207
> Bethesda, MD 20892, USA
> TEL: (+1) 301-435-2986
> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>
> Jairo Navarro
> UCSC Genome Browser
>
>
> On Mon, Dec 11, 2023 at 11:41 AM 'Hoover, David (NIH/CIT) [E]' via UCSC Genome Browser Mirror-Specific Support <genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu>> wrote:
>
> Hi all,
>
> We recently migrated our webserver hosting a local GB mirror from centos7 to rocky8, and now we are seeing a response slowdown for custom tracks. When the custom tracks are loaded, typically we see the error message in the browser window:
>
> Error unexpected end of input reading http header on https://...
>
> The custom track data is stored on a different webserver. I can create the custom tracks on the UCSC site and load them using the remote URL without any problem, so I don't think it is the remote webserver.
>
> Do you know how to debug the problem of slow custom track loading?
>
> David
> --
> David Hoover, Ph.D.
> Computational Biologist
> High Performance Computing Services,
> Center for Information Technology,
> National Institutes of Health
> 12 South Dr., Rm 2N207
> Bethesda, MD 20892, USA
> TEL: (+1) 301-435-2986
>
> --
>
> ---
> You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu>.
> --
>
> ---
> You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/0b5fd578-6174-f7bc-aa9f-63976a4f489a%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/0b5fd578-6174-f7bc-aa9f-63976a4f489a%40hpc.nih.gov>.
Hoover, David (NIH/CIT) [E]
Dec 12, 2023, 1:15:07 PM12/12/23
to Jairo Navarro Gonzalez, genome...@soe.ucsc.edu
Jairo,
I am very certain that our remote dataserver (https://hpc.nih.gov) has nothing to do with the problem. Like I said before, I can create and load custom tracks on the UCSC site using hpc.nih.gov as the remote data source (so-called "bigDataUrl") with no problems.
I don't know if I mentioned, when I first migrated our mirror webserver to rocky8 and compiled the GB on rocky8, custom track loading resulted in memory segfaults. This was v456 of the GB. Luckily v457 had already been released, and when I compiled that for rocky8, it ran (at least with my tests) normally. I strongly suspect the fault lies with either the hgTracks CGI executable, or our webserver itself, or both.
Is there any way of compiling the CGI executables in a way that makes them report their actions/timings? I've tried changing the values for the sleep1000() function in hgTracks.c (line 7845) and searchTracks.c (line 405), but this did not affect its behavior. I don't want to throw darts and hope something helps.
David
On 12/11/2023 7:54 PM, Jairo Navarro Gonzalez wrote:
> To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/0b5fd578-6174-f7bc-aa9f-63976a4f489a%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/0b5fd578-6174-f7bc-aa9f-63976a4f489a%40hpc.nih.gov>.
I am very certain that our remote dataserver (https://hpc.nih.gov) has nothing to do with the problem. Like I said before, I can create and load custom tracks on the UCSC site using hpc.nih.gov as the remote data source (so-called "bigDataUrl") with no problems.
I don't know if I mentioned, when I first migrated our mirror webserver to rocky8 and compiled the GB on rocky8, custom track loading resulted in memory segfaults. This was v456 of the GB. Luckily v457 had already been released, and when I compiled that for rocky8, it ran (at least with my tests) normally. I strongly suspect the fault lies with either the hgTracks CGI executable, or our webserver itself, or both.
Is there any way of compiling the CGI executables in a way that makes them report their actions/timings? I've tried changing the values for the sleep1000() function in hgTracks.c (line 7845) and searchTracks.c (line 405), but this did not affect its behavior. I don't want to throw darts and hope something helps.
David
On 12/11/2023 7:54 PM, Jairo Navarro Gonzalez wrote:
> Hello,
>
> Thank you for using the UCSC Genome Browser and sending your inquiry.
>
> We believe a server configuration issue on your remote server caused the issue. We require the fileserver with your custom track data to accept byte-range requests to visualize it on the Genome Browser. To confirm, could you send us the output for the "curl" UNIX command for one of your bigDataUrls:
>
> curl -I <URL_to_your_file>
>
> Our code expects every line of the HTTP header to end with "\r\n" or "\n". It expects a final blank line ("\r\n" or "\n" only) to terminate the header. If it gets end-of-input before the final "\n" it produces your error.
>
> If you have any further questions, please reply to gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>.
>
> Thank you for using the UCSC Genome Browser and sending your inquiry.
>
> We believe a server configuration issue on your remote server caused the issue. We require the fileserver with your custom track data to accept byte-range requests to visualize it on the Genome Browser. To confirm, could you send us the output for the "curl" UNIX command for one of your bigDataUrls:
>
> curl -I <URL_to_your_file>
>
> Our code expects every line of the HTTP header to end with "\r\n" or "\n". It expects a final blank line ("\r\n" or "\n" only) to terminate the header. If it gets end-of-input before the final "\n" it produces your error.
>
> All messages sent to that address are archived on a publicly accessible Google Groups forum.
> If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>.
>
> Jairo Navarro
> UCSC Genome Browser
>
>
> On Mon, Dec 11, 2023 at 11:41 AM 'Hoover, David (NIH/CIT) [E]' via UCSC Genome Browser Mirror-Specific Support <genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu>> wrote:
>
> Hi all,
>
> We recently migrated our webserver hosting a local GB mirror from centos7 to rocky8, and now we are seeing a response slowdown for custom tracks. When the custom tracks are loaded, typically we see the error message in the browser window:
>
> Error unexpected end of input reading http header on https://...
>
> The custom track data is stored on a different webserver. I can create the custom tracks on the UCSC site and load them using the remote URL without any problem, so I don't think it is the remote webserver.
>
> Do you know how to debug the problem of slow custom track loading?
>
> David
> --
> David Hoover, Ph.D.
> Computational Biologist
> High Performance Computing Services,
> Center for Information Technology,
> National Institutes of Health
> 12 South Dr., Rm 2N207
> Bethesda, MD 20892, USA
> TEL: (+1) 301-435-2986
> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>
> Jairo Navarro
> UCSC Genome Browser
>
>
> On Mon, Dec 11, 2023 at 11:41 AM 'Hoover, David (NIH/CIT) [E]' via UCSC Genome Browser Mirror-Specific Support <genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu>> wrote:
>
> Hi all,
>
> We recently migrated our webserver hosting a local GB mirror from centos7 to rocky8, and now we are seeing a response slowdown for custom tracks. When the custom tracks are loaded, typically we see the error message in the browser window:
>
> Error unexpected end of input reading http header on https://...
>
> The custom track data is stored on a different webserver. I can create the custom tracks on the UCSC site and load them using the remote URL without any problem, so I don't think it is the remote webserver.
>
> Do you know how to debug the problem of slow custom track loading?
>
> David
> --
> David Hoover, Ph.D.
> Computational Biologist
> High Performance Computing Services,
> Center for Information Technology,
> National Institutes of Health
> 12 South Dr., Rm 2N207
> Bethesda, MD 20892, USA
> TEL: (+1) 301-435-2986
>
> --
>
> ---
> You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu>.
> --
>
> ---
> You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/0b5fd578-6174-f7bc-aa9f-63976a4f489a%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/0b5fd578-6174-f7bc-aa9f-63976a4f489a%40hpc.nih.gov>.
Belinda M. Giardine
Dec 12, 2023, 1:46:31 PM12/12/23
to 'Hoover, David (NIH/CIT) [E]' via UCSC Genome Browser Mirror-Specific Support, Jairo Navarro Gonzalez
I will be interested in hearing what you find out. We have something
similar happening with our mirror. The error is a timeout, and randomly
hits subtracks in a composite track when displayed in our mirror. Same
hub displays fine at UCSC. We thought it could possibly be just too much
load for our server.
Belinda
>> On Mon, Dec 11, 2023 at 11:41?AM 'Hoover, David (NIH/CIT) [E]' via UCSC
>>
>> The custom track data is stored on a different webserver.? I can create
> email to genome-mirro...@soe.ucsc.edu.
>
similar happening with our mirror. The error is a timeout, and randomly
hits subtracks in a composite track when displayed in our mirror. Same
hub displays fine at UCSC. We thought it could possibly be just too much
load for our server.
Belinda
>> Genome Browser Mirror-Specific Support <genome...@soe.ucsc.edu
>> <mailto:genome...@soe.ucsc.edu>> wrote:
>>
>> Hi all,
>>
>> We recently migrated our webserver hosting a local GB mirror from
>> centos7 to rocky8, and now we are seeing a response slowdown for custom
>> tracks.? When the custom tracks are loaded, typically we see the error
>> <mailto:genome...@soe.ucsc.edu>> wrote:
>>
>> Hi all,
>>
>> We recently migrated our webserver hosting a local GB mirror from
>> centos7 to rocky8, and now we are seeing a response slowdown for custom
>> message in the browser window:
>>
>> ? ?Error unexpected end of input reading http header on https://...
>>
>>
>> The custom track data is stored on a different webserver.? I can create
> To view this discussion on the web visit
> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/063de19a-cc4b-e62a-e6c0-b5d9943a330f%40hpc.nih.gov.
>
Hoover, David (NIH/CIT) [E]
Dec 13, 2023, 12:59:54 PM12/13/23
to genome...@soe.ucsc.edu
Now I am not so sure what is happening. Here are some observations:
* The timeout issue holds not just for custom tracks, for the track hubs as well
* On the UCSC site, I can load tracks and a hub hosted on our local dataserver (hpc.nih.gov), and these display normally
* The same tracks and hub do not load normally, suffer severe timeouts on our local mirror
* If a bigwig file is served on the same host as the mirror, it still shows request timeouts
* relocating the trash or udcCache directories to different filesystems has no effect
I've come to two possibilities. 1) Apache/2.4.37 running on rocky8 cripples byte-range address requests, or 2) the genome browser is not fully compatible with MariaDB/10.4.
Our database is quite substantial, and so I have not yet attempted migrating it back to MariaDB/10.3. That would be painful. I think there is a way of isolating just the custom tracks on their own database server.
* The timeout issue holds not just for custom tracks, for the track hubs as well
* On the UCSC site, I can load tracks and a hub hosted on our local dataserver (hpc.nih.gov), and these display normally
* The same tracks and hub do not load normally, suffer severe timeouts on our local mirror
* If a bigwig file is served on the same host as the mirror, it still shows request timeouts
* relocating the trash or udcCache directories to different filesystems has no effect
I've come to two possibilities. 1) Apache/2.4.37 running on rocky8 cripples byte-range address requests, or 2) the genome browser is not fully compatible with MariaDB/10.4.
Our database is quite substantial, and so I have not yet attempted migrating it back to MariaDB/10.3. That would be painful. I think there is a way of isolating just the custom tracks on their own database server.
Christopher Lee
Dec 13, 2023, 5:55:53 PM12/13/23
to Hoover, David (NIH/CIT) [E], genome...@soe.ucsc.edu
Hi Everyone,
David/Belinda does your apache log indicate any errors while you're
experiencing these problems? Do you have pstack installed and the
following two settings enabled in the sites hg.conf:
browser.dumpStack=on
signalsHandler=on
Have you experienced any problems communicating with these two servers
not through the genome browser, like using curl or rsync or wget or
even traceroute/tracepath?
Have you tried using http urls to load the custom tracks/hubs instead
of https urls?
Thanks,
On Wed, Dec 13, 2023 at 9:59 AM 'Hoover, David (NIH/CIT) [E]' via UCSC
David/Belinda does your apache log indicate any errors while you're
experiencing these problems? Do you have pstack installed and the
following two settings enabled in the sites hg.conf:
browser.dumpStack=on
signalsHandler=on
Have you experienced any problems communicating with these two servers
not through the genome browser, like using curl or rsync or wget or
even traceroute/tracepath?
Have you tried using http urls to load the custom tracks/hubs instead
of https urls?
Thanks,
On Wed, Dec 13, 2023 at 9:59 AM 'Hoover, David (NIH/CIT) [E]' via UCSC
> --
>
> ---
> You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu.
> To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov.
>
> ---
> You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
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Hiram Clawson
Dec 13, 2023, 11:57:29 PM12/13/23
to Christopher Lee, Hoover, David (NIH/CIT) [E], genome...@soe.ucsc.edu
Good Evening David:
It isn't necessary to compile anything special to get timing information
out of the browser. In your web browser for the URL it is using
to the browser, add the argument: measureTiming=1
to the URL and the resulting return web page from the browser will indicate
timings of various aspects of the work the browser did to construct
that page. Comparing a responsive browser site such as genome.ucsc.edu
with you local server should be instructive of where bottlenecks may reside.
I'm confused about how you have described the interaction. You have mentioned
'custom tracks' and database operations. Do you mean you have local database
tables for tracks you have generated locally and they are in trackDb definitions
to add them to the browser ? Or, are you submitting 'custom tracks' to
the custom track submission system, either ascii text files that are transmitted
to the browser via https access where they are loaded into the 'customTrash'
database server ? Or custom track 'track' definition lines that include
bigDataUrl locations to an https access.
On your server that is showing slow access behavior, check the apache logs to
see if it is encountering any unusual errors. And also check the apache error
logs on your browser apache server.
You can also use the 'curl' command on URLs to determine timing and performance,
and how they honor the 'byte-range' requests.
--Hiram
It isn't necessary to compile anything special to get timing information
out of the browser. In your web browser for the URL it is using
to the browser, add the argument: measureTiming=1
to the URL and the resulting return web page from the browser will indicate
timings of various aspects of the work the browser did to construct
that page. Comparing a responsive browser site such as genome.ucsc.edu
with you local server should be instructive of where bottlenecks may reside.
I'm confused about how you have described the interaction. You have mentioned
'custom tracks' and database operations. Do you mean you have local database
tables for tracks you have generated locally and they are in trackDb definitions
to add them to the browser ? Or, are you submitting 'custom tracks' to
the custom track submission system, either ascii text files that are transmitted
to the browser via https access where they are loaded into the 'customTrash'
database server ? Or custom track 'track' definition lines that include
bigDataUrl locations to an https access.
On your server that is showing slow access behavior, check the apache logs to
see if it is encountering any unusual errors. And also check the apache error
logs on your browser apache server.
You can also use the 'curl' command on URLs to determine timing and performance,
and how they honor the 'byte-range' requests.
--Hiram
Maximilian Haeussler
Dec 14, 2023, 12:11:01 PM12/14/23
to Hoover, David (NIH/CIT) [E], genome...@soe.ucsc.edu
Hi David,
here are a few more ideas:
The timeout issue holds not just for custom tracks, for the track hubs as well
I think this again shows that our udc.c / http.c / net.c etc networking code must have a problem, it has nothing to do with hgCustom or custom tracks or Mysql
* On the UCSC site, I can load tracks and a hub hosted on our local dataserver (hpc.nih.gov), and these display normally
* The same tracks and hub do not load normally, suffer severe timeouts on our local mirror
This is essential: are these only timeouts or actual crashes, and if so, which error messages and if so, is there something in the apache log?
I think this is still not clear from your descriptions.
Can you run hubCheck on the failing hubs and that works?
Also note that the genome browser uses massive parallel requests to download the files, see this setting in hg.conf:
# Parallel fetching of remote network resources using bigDataUrl such as trackHubs and customTracks
# how many threads to use (set to 0 to disable)
parallelFetch.threads=100
# how long to wait in seconds for parallel fetch to finish
parallelFetch.timeout=90
# how many threads to use (set to 0 to disable)
parallelFetch.threads=100
# how long to wait in seconds for parallel fetch to finish
parallelFetch.timeout=90
So a curl or wget request is different, on our public site we're pulling the files with 100 parallel threads.
Are you also using this setting on your mirror? Do you want to try to set it to 0 to see if
the multithreading is causing problems?
* If a bigwig file is served on the same host as the mirror, it still shows request timeouts
Good idea. So this means it has nothing to do with your network.
To get around all the networking code and Apache (which should also be faster...), you can use this hg.conf setting and point it to a directory on your disk:
udc.localDir=/myFiles/
This allows you to load custom track files directly from disk with a custom track line like this in hgCustom:
track name=test bigDataUrl=/myFiles/test.bigWig
Do you want to try this setting? If it works, you can eliminate udc, sparse files and Apache.
* relocating the trash or udcCache directories to different filesystems has no effect
Good idea. So this means that the sparse files that udc.c uses are not the problem.
I've come to two possibilities. 1) Apache/2.4.37 running on rocky8 cripples byte-range address requests, or 2) the genome browser is not fully compatible with MariaDB/10.4.
I don't believe either of these hypotheses. Rocky 8 is pretty common and stable, a byte-range problem should have come up before (I just googled and found nothing) and the problem is independent from MariaDb.
Our database is quite substantial, and so I have not yet attempted migrating it back to MariaDB/10.3. That would be painful. I think there is a way of isolating just the custom tracks on their own database server.
I'd not migrate. We'll figure it out, we just need a way to reproduce it or to narrow it down at least.
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Hoover, David (NIH/CIT) [E]
Dec 14, 2023, 12:11:07 PM12/14/23
to genome...@soe.ucsc.edu
I don't know what those two setting are supposed to do, they do nothing for me.
I can use wget or curl to download the data with no issues. In fact, I can use byte-range addressing to pull down chunks:
curl -i --header "Range: bytes=1000-1500" https://hpc.nih.gov/index.html
There is no issue with the network, as I said previously. If the custom track bigwig file is on the same server as the mirror host, I still see these problems.
We are not able to switch between http and https, that is against security policy.
One breakthrough -- hgTracks works perfectly on centos7, but not on rocky8. This issue only arose because we migrated our mirror server from centos7 to rocky8, and this migration broke things.
David
I can use wget or curl to download the data with no issues. In fact, I can use byte-range addressing to pull down chunks:
curl -i --header "Range: bytes=1000-1500" https://hpc.nih.gov/index.html
There is no issue with the network, as I said previously. If the custom track bigwig file is on the same server as the mirror host, I still see these problems.
We are not able to switch between http and https, that is against security policy.
One breakthrough -- hgTracks works perfectly on centos7, but not on rocky8. This issue only arose because we migrated our mirror server from centos7 to rocky8, and this migration broke things.
David
Hoover, David (NIH/CIT) [E]
Dec 14, 2023, 12:11:13 PM12/14/23
to Hiram Clawson, Christopher Lee, genome...@soe.ucsc.edu
The problem has something to do with our rocky8 os. Up until Dec 3, our mirror server was running on centos7, and everything was fine. We have migrated our server to rocky8, and after that it is broken. This is surprising, since I understand UCSC is running on RHEL9.
Let me describe in full detail what is happening:
* load the browser (hgGateway)
* reset all user settings
* click 'Genome Browser' for mm10
* click 'My Data' --> 'Custom Tracks'
* paste my track definition and click submit
* this takes about 45 seconds to load, typically results in 'Show' in the error box
* click on 'go to first annotation'
* this takes about 45 seconds to load
* usually this results in a yellow error band in place of the track data
* sometimes 'Error unexpected end of input'
* sometimes 'Error (Connection reset by peer)'
* after many browser reloads (at least 3), the track may eventually be displayed
* changing the position will result in another yellow error band
I have used strace to watch what hgTracks is doing. It first connects to the database and downloads some information, but then it marches along through ~400 steps of sleeping with a timeout until giving up.
From the Apache logs, it looks as if hgTracks connects to the data server, but then does nothing until being disconnected (~20 seconds). This results in a 408 error.
Setting parallelFetch.threads=0 does not help.
Setting parallelFetch.timeout to a value less than 20 seconds typically results in the yellow error band displaying 'Timeout'.
I don't know what it is, but it seems that remote data requests from hgTracks on rocky8 is broken, but unfortunately in a random way. Sometimes it works, usually it does not.
David
Let me describe in full detail what is happening:
* load the browser (hgGateway)
* reset all user settings
* click 'Genome Browser' for mm10
* click 'My Data' --> 'Custom Tracks'
* paste my track definition and click submit
* this takes about 45 seconds to load, typically results in 'Show' in the error box
* click on 'go to first annotation'
* this takes about 45 seconds to load
* usually this results in a yellow error band in place of the track data
* sometimes 'Error unexpected end of input'
* sometimes 'Error (Connection reset by peer)'
* after many browser reloads (at least 3), the track may eventually be displayed
* changing the position will result in another yellow error band
I have used strace to watch what hgTracks is doing. It first connects to the database and downloads some information, but then it marches along through ~400 steps of sleeping with a timeout until giving up.
From the Apache logs, it looks as if hgTracks connects to the data server, but then does nothing until being disconnected (~20 seconds). This results in a 408 error.
Setting parallelFetch.threads=0 does not help.
Setting parallelFetch.timeout to a value less than 20 seconds typically results in the yellow error band displaying 'Timeout'.
I don't know what it is, but it seems that remote data requests from hgTracks on rocky8 is broken, but unfortunately in a random way. Sometimes it works, usually it does not.
David
Belinda M. Giardine
Dec 14, 2023, 1:42:02 PM12/14/23
to Maximilian Haeussler, Hoover, David (NIH/CIT) [E], genome...@soe.ucsc.edu
On Thu, 14 Dec 2023, 'Maximilian Haeussler' via UCSC Genome Browser Mirror-Specific Support wrote:
> trackHubs and customTracks
> # how many threads to use (set to 0 to disable)
> parallelFetch.threads=100
> # how long to wait in seconds for parallel fetch to finish
> parallelFetch.timeout=90
overloaded as I first suspected it should help.
...
> I'd not migrate. We'll figure it out, we just need a way to reproduce it or
> to narrow it down at least.
>
It can be reproduced at our mirror.
> to narrow it down at least.
>
What works:
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hubUrl=https://usevision.org/data/trackHub/hub.txt
Open any number of the Signal* tracks. I even did all 200+ without
problems.
What fails:
http://main.genome-browser.bx.psu.edu/cgi-bin/hgTracks?db=hg38&hubUrl=https://usevision.org/data/trackHub/hub.txt
Open any number of the Signal* tracks. I did it just now to make sure it
still fails, and it is even failing on some of the bigBed files that are
on by default.
From the logs:
[Thu Dec 14 12:25:01.663153 2023] [cgi:error] [pid 9601] [client
73.175.4.89:49560] AH01215: :
/afs/bx.psu.edu/service/web/sites/main.genome-browser.bx.psu.edu/cgi-bin/hgTracks,
referer:
https://main.genome-browser.bx.psu.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr9%3A133252000%2D133280861&hgsid=226993_IJg2hC4l2olVY7hasRpZAHYbqacX
Belinda
Belinda M. Giardine
Dec 14, 2023, 1:42:07 PM12/14/23
to Maximilian Haeussler, Hoover, David (NIH/CIT) [E], genome...@soe.ucsc.edu
It seems our hg.conf was missing these options entirely. When I put them
in and adjusted them to no threading and 150 for timeout, our private
server was able to load 20 tracks without errors. It may be helpful to
make the default be no threading if the parameter is missing.
Thanks,
Belinda
in and adjusted them to no threading and 150 for timeout, our private
server was able to load 20 tracks without errors. It may be helpful to
make the default be no threading if the parameter is missing.
Thanks,
Belinda
Mark Diekhans
Dec 15, 2023, 1:11:08 PM12/15/23
to Hoover, David (NIH/CIT) [E], Hiram Clawson, Christopher Lee, genome...@soe.ucsc.edu
Perhaps this is a problem with the MariaDB server.
These two hg.conf settings will give you more information in
the apache log files:
JKSQL_TRACE=on
JKSQL_PROF=on
TRACE will show you the SQL commands, so you can try them manually.
Mark
Maximilian Haeussler
Dec 15, 2023, 1:11:12 PM12/15/23
to Belinda M. Giardine, Hoover, David (NIH/CIT) [E], genome...@soe.ucsc.edu
Hi David,
(and Belinda: the default value for parallelThreads is 20, but I think David, you've already determined that reducing it does not help and for Belinda it seems to help, which suggests a problem with the server from which the files are loaded, unless that server has not been touched or upgraded at all)
Can you try the udc.localDir=xxx statement that I suggested? It will allow you to circumvent the entire caching system and load files from your local disk. We can eliminate then the udc and caching system of remote files (hubs and big* custom track files are using exactly the same loading code).
We'll also try the genome browser on Rocky8 here.
best
Max
Hoover, David (NIH/CIT) [E]
Dec 18, 2023, 12:50:46 PM12/18/23
to Mark Diekhans, Hiram Clawson, Christopher Lee, genome...@soe.ucsc.edu
Alas, no, it is not the MariaDB server, for a few reasons.
* If we move the mirror server from rocky8 to centos7, there are no errors.
* The errors only occur with custom tracks and hub tracks, whereas ordinary tracks to not have errors.
* The sql statements written to the error log run normally with no errors on their own.
* If we move the mirror server from rocky8 to centos7, there are no errors.
* The errors only occur with custom tracks and hub tracks, whereas ordinary tracks to not have errors.
* The sql statements written to the error log run normally with no errors on their own.
Belinda M. Giardine
Dec 18, 2023, 2:31:57 PM12/18/23
to Hoover, David (NIH/CIT) [E], Mark Diekhans, Hiram Clawson, Christopher Lee, genome...@soe.ucsc.edu
I would guess a bug with threads, similar to what we had. It isn't just
load because 4 threads which should not be a problem still errors just not
as frequently. Only no threads seems to completely work. We recently
upgraded our server as well. Unfortunately I don't know the versions.
Belinda
>>>> out of the browser.? In your web browser for the URL it is using
>>>> to the browser, add the argument:? measureTiming=1
>>>> mentioned
>>>> 'custom tracks' and database operations.? Do you mean you have local
>>>>>> Now I am not so sure what is happening.? Here are some observations:
> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov.
>
>
load because 4 threads which should not be a problem still errors just not
as frequently. Only no threads seems to completely work. We recently
upgraded our server as well. Unfortunately I don't know the versions.
Belinda
>>>> to the browser, add the argument:? measureTiming=1
>>>> to the URL and the resulting return web page from the browser will
>>>> indicate
>>>> timings of various aspects of the work the browser did to construct
>>>> that page.? Comparing a responsive browser site such as genome.ucsc.edu
>>>> indicate
>>>> timings of various aspects of the work the browser did to construct
>>>> with you local server should be instructive of where bottlenecks may
>>>> reside.
>>>>
>>>> I'm confused about how you have described the interaction.? You have
>>>> reside.
>>>>
>>>> mentioned
>>>> 'custom tracks' and database operations.? Do you mean you have local
>>>> database
>>>> tables for tracks you have generated locally and they are in trackDb
>>>> definitions
>>>> to add them to the browser ?? Or, are you submitting 'custom tracks' to
>>>> tables for tracks you have generated locally and they are in trackDb
>>>> definitions
>>>> the custom track submission system, either ascii text files that are
>>>> transmitted
>>>> to the browser via https access where they are loaded into the
>>>> 'customTrash'
>>>> database server ?? Or custom track 'track' definition lines that include
>>>> transmitted
>>>> to the browser via https access where they are loaded into the
>>>> 'customTrash'
>>>> bigDataUrl locations to an https access.
>>>>
>>>> On your server that is showing slow access behavior, check the apache
>>>> logs to
>>>> see if it is encountering any unusual errors.? And also check the apache
>>>>
>>>> On your server that is showing slow access behavior, check the apache
>>>> logs to
>>>> error
>>>> logs on your browser apache server.
>>>>
>>>> You can also use the 'curl' command on URLs to determine timing and
>>>> performance,
>>>> and how they honor the 'byte-range' requests.
>>>>
>>>> --Hiram
>>>>
>>>> On 12/13/23 2:55 PM, 'Christopher Lee' via UCSC Genome Browser
>>>> Mirror-Specific Support wrote:
>>>>> Hi Everyone,
>>>>>
>>>>> David/Belinda does your apache log indicate any errors while you're
>>>>> experiencing these problems? Do you have pstack installed and the
>>>>> following two settings enabled in the sites hg.conf:
>>>>> browser.dumpStack=on
>>>>> signalsHandler=on
>>>>>
>>>>> Have you experienced any problems communicating with these two servers
>>>>> not through the genome browser, like using curl or rsync or wget or
>>>>> even traceroute/tracepath?
>>>>>
>>>>> Have you tried using http urls to load the custom tracks/hubs instead
>>>>> of https urls?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> On Wed, Dec 13, 2023 at 9:59?AM 'Hoover, David (NIH/CIT) [E]' via UCSC
>>>> logs on your browser apache server.
>>>>
>>>> You can also use the 'curl' command on URLs to determine timing and
>>>> performance,
>>>> and how they honor the 'byte-range' requests.
>>>>
>>>> --Hiram
>>>>
>>>> On 12/13/23 2:55 PM, 'Christopher Lee' via UCSC Genome Browser
>>>> Mirror-Specific Support wrote:
>>>>> Hi Everyone,
>>>>>
>>>>> David/Belinda does your apache log indicate any errors while you're
>>>>> experiencing these problems? Do you have pstack installed and the
>>>>> following two settings enabled in the sites hg.conf:
>>>>> browser.dumpStack=on
>>>>> signalsHandler=on
>>>>>
>>>>> Have you experienced any problems communicating with these two servers
>>>>> not through the genome browser, like using curl or rsync or wget or
>>>>> even traceroute/tracepath?
>>>>>
>>>>> Have you tried using http urls to load the custom tracks/hubs instead
>>>>> of https urls?
>>>>>
>>>>> Thanks,
>>>>>
>>>>>> Now I am not so sure what is happening.? Here are some observations:
>>>>>>
>>>>>> * The timeout issue holds not just for custom tracks, for the track
>>>>>> hubs as well
>>>>>> * On the UCSC site, I can load tracks and a hub hosted on our local
>>>>>> dataserver (hpc.nih.gov), and these display normally
>>>>>> * The same tracks and hub do not load normally, suffer severe timeouts
>>>>>> on our local mirror
>>>>>> * If a bigwig file is served on the same host as the mirror, it still
>>>>>> shows request timeouts
>>>>>> * relocating the trash or udcCache directories to different filesystems
>>>>>> has no effect
>>>>>>
>>>>>> I've come to two possibilities.? 1) Apache/2.4.37 running on rocky8
>>>>>> * The timeout issue holds not just for custom tracks, for the track
>>>>>> hubs as well
>>>>>> * On the UCSC site, I can load tracks and a hub hosted on our local
>>>>>> dataserver (hpc.nih.gov), and these display normally
>>>>>> * The same tracks and hub do not load normally, suffer severe timeouts
>>>>>> on our local mirror
>>>>>> * If a bigwig file is served on the same host as the mirror, it still
>>>>>> shows request timeouts
>>>>>> * relocating the trash or udcCache directories to different filesystems
>>>>>> has no effect
>>>>>>
>>>>>> cripples byte-range address requests, or 2) the genome browser is not
>>>>>> fully compatible with MariaDB/10.4.
>>>>>>
>>>>>> Our database is quite substantial, and so I have not yet attempted
>>>>>> migrating it back to MariaDB/10.3.? That would be painful.? I think
>>>>>> fully compatible with MariaDB/10.4.
>>>>>>
>>>>>> Our database is quite substantial, and so I have not yet attempted
>
>
Maximilian Haeussler
Dec 22, 2023, 1:13:14 PM12/22/23
to Belinda M. Giardine, Hoover, David (NIH/CIT) [E], Mark Diekhans, Hiram Clawson, Christopher Lee, genome...@soe.ucsc.edu
David and Belinda,
thank you for your patience with this, it's hard to debug if we don't have access to a machine and can't reproduce the problem. We don't think it's Rocky 9 itself (trying with a VM).
Are you both building your own binaries from the source code or are you using our pre-built binaries?
thanks
Max
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu.
Mark Diekhans
Dec 22, 2023, 1:13:17 PM12/22/23
to Maximilian Haeussler, Belinda M. Giardine, Hoover, David (NIH/CIT) [E], Mark Diekhans, Hiram Clawson, Christopher Lee, genome...@soe.ucsc.edu
Also, can you please do the database test suggestion I previous
sent. This behavior is similar to what was experienced when we
had a network issue connecting to the mysql server.
> > .
> > >
> > > --
> > > David Hoover, Ph.D.
> > > Computational Biologist
> > > High Performance Computing Services,
> > > Center for Information Technology,
> > > National Institutes of Health
> > > 12 South Dr., Rm 2N207
> > > Bethesda, MD 20892, USA
> > > TEL: (+1) 301-435-2986
> > > Email: hoov...@hpc.nih.gov
> > >
> > > --
> > >
> > > --- You received this message because you are subscribed to the Google
> > Groups
> > > "UCSC Genome Browser Mirror-Specific Support" group.
> > > To unsubscribe from this group and stop receiving emails from it, send
> > an
> > > email to genome-mirro...@soe.ucsc.edu.
> > > To view this discussion on the web visit
> > >
> > https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov
> > > --
> > > David Hoover, Ph.D.
> > > Computational Biologist
> > > High Performance Computing Services,
> > > Center for Information Technology,
> > > National Institutes of Health
> > > 12 South Dr., Rm 2N207
> > > Bethesda, MD 20892, USA
> > > TEL: (+1) 301-435-2986
> > > Email: hoov...@hpc.nih.gov
> > >
> > > --
> > >
> > > --- You received this message because you are subscribed to the Google
> > Groups
> > > "UCSC Genome Browser Mirror-Specific Support" group.
> > > To unsubscribe from this group and stop receiving emails from it, send
> > an
> > > email to genome-mirro...@soe.ucsc.edu.
> > > To view this discussion on the web visit
> > >
> > .
> > >
> > >
> >
> > --
> >
> > ---
> > You received this message because you are subscribed to the Google Groups
> > "UCSC Genome Browser Mirror-Specific Support" group.
> > To unsubscribe from this group and stop receiving emails from it, send an
> > email to genome-mirro...@soe.ucsc.edu.
> > To view this discussion on the web visit
> > https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu
> > >
> >
> > --
> >
> > ---
> > You received this message because you are subscribed to the Google Groups
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> > To unsubscribe from this group and stop receiving emails from it, send an
> > email to genome-mirro...@soe.ucsc.edu.
> > To view this discussion on the web visit
> > .
> >
Maximilian Haeussler
Dec 22, 2023, 1:13:19 PM12/22/23
to Mark Diekhans, Belinda M. Giardine, Hoover, David (NIH/CIT) [E], Hiram Clawson, Christopher Lee, genome...@soe.ucsc.edu
Hi David,
I have installed the browser on a fresh Rocky 9 VM and loaded a few public track hubs and all of them worked.
But I used our pre-built mostly-static binaries from hgdownload.soe.ucsc.edu, did you use those or did you build the binaries yourself?
Hoover, David (NIH/CIT) [E]
Dec 22, 2023, 4:01:37 PM12/22/23
to Maximilian Haeussler, Mark Diekhans, Belinda M. Giardine, Hiram Clawson, Christopher Lee, genome...@soe.ucsc.edu
I build the binaries myself on rocky8. I have not yet tried the GBIB, and I don't know where the binaries for hgTracks or hgCustom are located.
One thing I will try is to build the browser in Singularity. We can't use VirtualBox or Docker.
David
On 12/22/2023 12:58 PM, 'Maximilian Haeussler' via UCSC Genome Browser Mirror-Specific Support wrote:
> Hi David,
> I have installed the browser on a fresh Rocky 9 VM and loaded a few public track hubs and all of them worked.
>
> But I used our pre-built mostly-static binaries from hgdownload.soe.ucsc.edu <http://hgdownload.soe.ucsc.edu>, did you use those or did you build the binaries yourself?
> > > genome.ucsc.edu <http://genome.ucsc.edu>
> > > >>>>> Genome Browser Mirror-Specific Support <genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu>>
> > > >>>>>> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>
> To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fynWE87SnNSbmAyGSO9RdeXx%3DR52r3Zd19ZOWbJjstfWQ%40mail.gmail.com <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fynWE87SnNSbmAyGSO9RdeXx%3DR52r3Zd19ZOWbJjstfWQ%40mail.gmail.com?utm_medium=email&utm_source=footer>.
One thing I will try is to build the browser in Singularity. We can't use VirtualBox or Docker.
David
On 12/22/2023 12:58 PM, 'Maximilian Haeussler' via UCSC Genome Browser Mirror-Specific Support wrote:
> Hi David,
> I have installed the browser on a fresh Rocky 9 VM and loaded a few public track hubs and all of them worked.
>
>
> On Fri, Dec 22, 2023 at 5:51 PM Mark Diekhans <ma...@ucsc.edu <mailto:ma...@ucsc.edu>> wrote:
>
>
> Also, can you please do the database test suggestion I previous
> sent. This behavior is similar to what was experienced when we
> had a network issue connecting to the mysql server.
>
>
> Maximilian Haeussler <mhae...@ucsc.edu <mailto:mhae...@ucsc.edu>> writes:
> > David and Belinda,
> > thank you for your patience with this, it's hard to debug if we don't have
> > access to a machine and can't reproduce the problem. We don't think it's
> > Rocky 9 itself (trying with a VM).
> > Are you both building your own binaries from the source code or are you
> > using our pre-built binaries?
> > thanks
> > Max
> >
> > On Mon, Dec 18, 2023 at 8:31 PM Belinda M. Giardine <giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>>
> On Fri, Dec 22, 2023 at 5:51 PM Mark Diekhans <ma...@ucsc.edu <mailto:ma...@ucsc.edu>> wrote:
>
>
> Also, can you please do the database test suggestion I previous
> sent. This behavior is similar to what was experienced when we
> had a network issue connecting to the mysql server.
>
>
> Maximilian Haeussler <mhae...@ucsc.edu <mailto:mhae...@ucsc.edu>> writes:
> > David and Belinda,
> > thank you for your patience with this, it's hard to debug if we don't have
> > access to a machine and can't reproduce the problem. We don't think it's
> > Rocky 9 itself (trying with a VM).
> > Are you both building your own binaries from the source code or are you
> > using our pre-built binaries?
> > thanks
> > Max
> >
> > > >>>>> wrote:
> > > >>>>>>
> > > >>>>>> Now I am not so sure what is happening.? Here are some observations:
> > > >>>>>>
> > > >>>>>> * The timeout issue holds not just for custom tracks, for the track
> > > >>>>>> hubs as well
> > > >>>>>> * On the UCSC site, I can load tracks and a hub hosted on our local
> > > >>>>>> dataserver (hpc.nih.gov <http://hpc.nih.gov>), and these display normally
> > > >>>>>>
> > > >>>>>> Now I am not so sure what is happening.? Here are some observations:
> > > >>>>>>
> > > >>>>>> * The timeout issue holds not just for custom tracks, for the track
> > > >>>>>> hubs as well
> > > >>>>>> * On the UCSC site, I can load tracks and a hub hosted on our local
> > > >>>>>>
> > > >>>>>> --
> > > >>>>>>
> > > >>>>>> ---
> > > >>>>>> You received this message because you are subscribed to the Google
> > > >>>>>> Groups "UCSC Genome Browser Mirror-Specific Support" group.
> > > >>>>>> To unsubscribe from this group and stop receiving emails from it,
> > > send
> > > >>>>>> an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu>.
> > > >>>>>> --
> > > >>>>>>
> > > >>>>>> ---
> > > >>>>>> You received this message because you are subscribed to the Google
> > > >>>>>> Groups "UCSC Genome Browser Mirror-Specific Support" group.
> > > >>>>>> To unsubscribe from this group and stop receiving emails from it,
> > > send
> > > >>>>>> To view this discussion on the web visit
> > > >>>>>>
> > > https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov>
> > > >>>>>>
> > > .
> > > >>>>>
> > > >>>
> > > >>> --
> > > >>> David Hoover, Ph.D.
> > > >>> Computational Biologist
> > > >>> High Performance Computing Services,
> > > >>> Center for Information Technology,
> > > >>> National Institutes of Health
> > > >>> 12 South Dr., Rm 2N207
> > > >>> Bethesda, MD 20892, USA
> > > >>> TEL: (+1) 301-435-2986
> > > >>> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>
> > > >>>>>
> > > >>>
> > > >>> --
> > > >>> David Hoover, Ph.D.
> > > >>> Computational Biologist
> > > >>> High Performance Computing Services,
> > > >>> Center for Information Technology,
> > > >>> National Institutes of Health
> > > >>> 12 South Dr., Rm 2N207
> > > >>> Bethesda, MD 20892, USA
> > > >>> TEL: (+1) 301-435-2986
> > > >>>
> > > >>> --
> > > >>>
> > > >>> ---
> > > >>> You received this message because you are subscribed to the Google
> > > Groups
> > > >>> "UCSC Genome Browser Mirror-Specific Support" group.
> > > >>> To unsubscribe from this group and stop receiving emails from it, send
> > > an
> > > >>> email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu>.
> > > >>> --
> > > >>>
> > > >>> ---
> > > >>> You received this message because you are subscribed to the Google
> > > Groups
> > > >>> "UCSC Genome Browser Mirror-Specific Support" group.
> > > >>> To unsubscribe from this group and stop receiving emails from it, send
> > > an
> > > >>> To view this discussion on the web visit
> > > >>>
> > > https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov>
> > > >>>
> > > .
> > > >
> > > > --
> > > > David Hoover, Ph.D.
> > > > Computational Biologist
> > > > High Performance Computing Services,
> > > > Center for Information Technology,
> > > > National Institutes of Health
> > > > 12 South Dr., Rm 2N207
> > > > Bethesda, MD 20892, USA
> > > > TEL: (+1) 301-435-2986
> > > > Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>
> > > >
> > > > --
> > > > David Hoover, Ph.D.
> > > > Computational Biologist
> > > > High Performance Computing Services,
> > > > Center for Information Technology,
> > > > National Institutes of Health
> > > > 12 South Dr., Rm 2N207
> > > > Bethesda, MD 20892, USA
> > > > TEL: (+1) 301-435-2986
> > > >
> > > > --
> > > >
> > > > --- You received this message because you are subscribed to the Google
> > > Groups
> > > > "UCSC Genome Browser Mirror-Specific Support" group.
> > > > To unsubscribe from this group and stop receiving emails from it, send
> > > an
> > > > email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu>.
> > > > --
> > > >
> > > > --- You received this message because you are subscribed to the Google
> > > Groups
> > > > "UCSC Genome Browser Mirror-Specific Support" group.
> > > > To unsubscribe from this group and stop receiving emails from it, send
> > > an
> > > > To view this discussion on the web visit
> > > >
> > > https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov>
> > > >
> > > .
> > > >
> > > >
> > >
> > > --
> > >
> > > ---
> > > You received this message because you are subscribed to the Google Groups
> > > "UCSC Genome Browser Mirror-Specific Support" group.
> > > To unsubscribe from this group and stop receiving emails from it, send an
> > > email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu>.
> > > >
> > > >
> > >
> > > --
> > >
> > > ---
> > > You received this message because you are subscribed to the Google Groups
> > > "UCSC Genome Browser Mirror-Specific Support" group.
> > > To unsubscribe from this group and stop receiving emails from it, send an
> > > To view this discussion on the web visit
> > > https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu>
> > > .
> > >
>
> --
>
> ---
> You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirro...@soe.ucsc.edu>.
> > >
>
> --
>
> ---
> You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fynWE87SnNSbmAyGSO9RdeXx%3DR52r3Zd19ZOWbJjstfWQ%40mail.gmail.com <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fynWE87SnNSbmAyGSO9RdeXx%3DR52r3Zd19ZOWbJjstfWQ%40mail.gmail.com?utm_medium=email&utm_source=footer>.
Hoover, David (NIH/CIT) [E]
Dec 22, 2023, 4:01:41 PM12/22/23
to Maximilian Haeussler, Belinda M. Giardine, Mark Diekhans, Hiram Clawson, Christopher Lee, genome...@soe.ucsc.edu
We are not using RHEL9 nor rocky 9. We are using rocky 8. I can compile it on both centos 7 and rocky 8, and it runs fine on centos 7, but rocky 8 is where it is broken.
David
On 12/22/2023 4:07 AM, 'Maximilian Haeussler' via UCSC Genome Browser Mirror-Specific Support wrote:
> David and Belinda,
> thank you for your patience with this, it's hard to debug if we don't have access to a machine and can't reproduce the problem. We don't think it's Rocky 9 itself (trying with a VM).
> Are you both building your own binaries from the source code or are you using our pre-built binaries?
> thanks
> Max
>
> >>>> that page.? Comparing a responsive browser site such as genome.ucsc.edu <http://genome.ucsc.edu>
> >>>>> Genome Browser Mirror-Specific Support <genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu>>
> To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu>.
> To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fwnfz7UdN0WDjDTx5SekYBmcO_ULofXGwgsz95Yq6FhBQ%40mail.gmail.com <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fwnfz7UdN0WDjDTx5SekYBmcO_ULofXGwgsz95Yq6FhBQ%40mail.gmail.com?utm_medium=email&utm_source=footer>.
David
On 12/22/2023 4:07 AM, 'Maximilian Haeussler' via UCSC Genome Browser Mirror-Specific Support wrote:
> David and Belinda,
> thank you for your patience with this, it's hard to debug if we don't have access to a machine and can't reproduce the problem. We don't think it's Rocky 9 itself (trying with a VM).
> Are you both building your own binaries from the source code or are you using our pre-built binaries?
> thanks
> Max
>
> On Mon, Dec 18, 2023 at 8:31 PM Belinda M. Giardine <giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>> wrote:
>
> I would guess a bug with threads, similar to what we had. It isn't just
> load because 4 threads which should not be a problem still errors just not
> as frequently. Only no threads seems to completely work. We recently
> upgraded our server as well. Unfortunately I don't know the versions.
>
> Belinda
>
>
> On Mon, 18 Dec 2023, 'Hoover, David (NIH/CIT) [E]' via UCSC Genome Browser Mirror-Specific Support wrote:
>
> > Alas, no, it is not the MariaDB server, for a few reasons.
> >
> > * If we move the mirror server from rocky8 to centos7, there are no errors.
> > * The errors only occur with custom tracks and hub tracks, whereas ordinary
> > tracks to not have errors.
> > * The sql statements written to the error log run normally with no errors on
> > their own.
> >
> > On 12/15/2023 10:42 AM, Mark Diekhans wrote:
> >>
> >> Perhaps this is a problem with the MariaDB server.
> >>
> >> These two hg.conf settings will give you more information in
> >> the apache log files:
> >>
> >> JKSQL_TRACE=on
> >> JKSQL_PROF=on
> >>
> >> TRACE will show you the SQL commands, so you can try them manually.
> >>
> >> Mark
> >>
> >>
> >> 'Hoover, David (NIH/CIT) [E]' via UCSC Genome Browser Mirror-Specific
>
> I would guess a bug with threads, similar to what we had. It isn't just
> load because 4 threads which should not be a problem still errors just not
> as frequently. Only no threads seems to completely work. We recently
> upgraded our server as well. Unfortunately I don't know the versions.
>
> Belinda
>
>
> On Mon, 18 Dec 2023, 'Hoover, David (NIH/CIT) [E]' via UCSC Genome Browser Mirror-Specific Support wrote:
>
> > Alas, no, it is not the MariaDB server, for a few reasons.
> >
> > * If we move the mirror server from rocky8 to centos7, there are no errors.
> > * The errors only occur with custom tracks and hub tracks, whereas ordinary
> > tracks to not have errors.
> > * The sql statements written to the error log run normally with no errors on
> > their own.
> >
> > On 12/15/2023 10:42 AM, Mark Diekhans wrote:
> >>
> >> Perhaps this is a problem with the MariaDB server.
> >>
> >> These two hg.conf settings will give you more information in
> >> the apache log files:
> >>
> >> JKSQL_TRACE=on
> >> JKSQL_PROF=on
> >>
> >> TRACE will show you the SQL commands, so you can try them manually.
> >>
> >> Mark
> >>
> >>
> >> 'Hoover, David (NIH/CIT) [E]' via UCSC Genome Browser Mirror-Specific
> >>>>> wrote:
> >>>>>>
> >>>>>> Now I am not so sure what is happening.? Here are some observations:
> >>>>>>
> >>>>>> * The timeout issue holds not just for custom tracks, for the track
> >>>>>> hubs as well
> >>>>>> * On the UCSC site, I can load tracks and a hub hosted on our local
> >>>>>> dataserver (hpc.nih.gov <http://hpc.nih.gov>), and these display normally
> >>>>>>
> >>>>>> Now I am not so sure what is happening.? Here are some observations:
> >>>>>>
> >>>>>> * The timeout issue holds not just for custom tracks, for the track
> >>>>>> hubs as well
> >>>>>> * On the UCSC site, I can load tracks and a hub hosted on our local
> >>>>>> * The same tracks and hub do not load normally, suffer severe timeouts
> >>>>>> on our local mirror
> >>>>>> * If a bigwig file is served on the same host as the mirror, it still
> >>>>>> shows request timeouts
> >>>>>> * relocating the trash or udcCache directories to different filesystems
> >>>>>> has no effect
> >>>>>>
> >>>>>> I've come to two possibilities.? 1) Apache/2.4.37 running on rocky8
> >>>>>> cripples byte-range address requests, or 2) the genome browser is not
> >>>>>> fully compatible with MariaDB/10.4.
> >>>>>>
> >>>>>> Our database is quite substantial, and so I have not yet attempted
> >>>>>> migrating it back to MariaDB/10.3.? That would be painful.? I think
> >>>>>> there is a way of isolating just the custom tracks on their own
> >>>>>> database server.
> >>>>>>
> >>>>>> David
> >>>>>> --
> >>>>>> David Hoover, Ph.D.
> >>>>>> Computational Biologist
> >>>>>> High Performance Computing Services,
> >>>>>> Center for Information Technology,
> >>>>>> National Institutes of Health
> >>>>>> 12 South Dr., Rm 2N207
> >>>>>> Bethesda, MD 20892, USA
> >>>>>> TEL: (+1) 301-435-2986
> >>>>>> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>
> >>>>>> on our local mirror
> >>>>>> * If a bigwig file is served on the same host as the mirror, it still
> >>>>>> shows request timeouts
> >>>>>> * relocating the trash or udcCache directories to different filesystems
> >>>>>> has no effect
> >>>>>>
> >>>>>> I've come to two possibilities.? 1) Apache/2.4.37 running on rocky8
> >>>>>> cripples byte-range address requests, or 2) the genome browser is not
> >>>>>> fully compatible with MariaDB/10.4.
> >>>>>>
> >>>>>> Our database is quite substantial, and so I have not yet attempted
> >>>>>> migrating it back to MariaDB/10.3.? That would be painful.? I think
> >>>>>> there is a way of isolating just the custom tracks on their own
> >>>>>> database server.
> >>>>>>
> >>>>>> David
> >>>>>> --
> >>>>>> David Hoover, Ph.D.
> >>>>>> Computational Biologist
> >>>>>> High Performance Computing Services,
> >>>>>> Center for Information Technology,
> >>>>>> National Institutes of Health
> >>>>>> 12 South Dr., Rm 2N207
> >>>>>> Bethesda, MD 20892, USA
> >>>>>> TEL: (+1) 301-435-2986
> >>>>>>
> >>>>>> --
> >>>>>>
> >>>>>> ---
> >>>>>> You received this message because you are subscribed to the Google
> >>>>>> Groups "UCSC Genome Browser Mirror-Specific Support" group.
> >>>>>> To unsubscribe from this group and stop receiving emails from it, send
> >>>>>> an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu>.
> >>>>>> --
> >>>>>>
> >>>>>> ---
> >>>>>> You received this message because you are subscribed to the Google
> >>>>>> Groups "UCSC Genome Browser Mirror-Specific Support" group.
> >>>>>> To unsubscribe from this group and stop receiving emails from it, send
> >>>>>> To view this discussion on the web visit
> >>>>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov>.
> >>>>>
> >>>
> >>> --
> >>> David Hoover, Ph.D.
> >>> Computational Biologist
> >>> High Performance Computing Services,
> >>> Center for Information Technology,
> >>> National Institutes of Health
> >>> 12 South Dr., Rm 2N207
> >>> Bethesda, MD 20892, USA
> >>> TEL: (+1) 301-435-2986
> >>> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>
> >>>
> >>> --
> >>> David Hoover, Ph.D.
> >>> Computational Biologist
> >>> High Performance Computing Services,
> >>> Center for Information Technology,
> >>> National Institutes of Health
> >>> 12 South Dr., Rm 2N207
> >>> Bethesda, MD 20892, USA
> >>> TEL: (+1) 301-435-2986
> >>>
> >>> --
> >>>
> >>> ---
> >>> You received this message because you are subscribed to the Google Groups
> >>> "UCSC Genome Browser Mirror-Specific Support" group.
> >>> To unsubscribe from this group and stop receiving emails from it, send an
> >>> email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu>.
> >>> --
> >>>
> >>> ---
> >>> You received this message because you are subscribed to the Google Groups
> >>> "UCSC Genome Browser Mirror-Specific Support" group.
> >>> To unsubscribe from this group and stop receiving emails from it, send an
> >>> To view this discussion on the web visit
> >>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov>.
> >
> > --
> > David Hoover, Ph.D.
> > Computational Biologist
> > High Performance Computing Services,
> > Center for Information Technology,
> > National Institutes of Health
> > 12 South Dr., Rm 2N207
> > Bethesda, MD 20892, USA
> > TEL: (+1) 301-435-2986
> > Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>
> > --
> > David Hoover, Ph.D.
> > Computational Biologist
> > High Performance Computing Services,
> > Center for Information Technology,
> > National Institutes of Health
> > 12 South Dr., Rm 2N207
> > Bethesda, MD 20892, USA
> > TEL: (+1) 301-435-2986
> >
> > --
> >
> > --- You received this message because you are subscribed to the Google Groups
> > "UCSC Genome Browser Mirror-Specific Support" group.
> > To unsubscribe from this group and stop receiving emails from it, send an
> > email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu>.
> > --
> >
> > --- You received this message because you are subscribed to the Google Groups
> > "UCSC Genome Browser Mirror-Specific Support" group.
> > To unsubscribe from this group and stop receiving emails from it, send an
> > To view this discussion on the web visit
> > https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov>.
> >
> >
>
> --
>
> ---
> You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu>.
> >
>
> --
>
> ---
> You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu>.
>
> --
>
> ---
> You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirro...@soe.ucsc.edu>.
> --
>
> ---
> You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fwnfz7UdN0WDjDTx5SekYBmcO_ULofXGwgsz95Yq6FhBQ%40mail.gmail.com <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fwnfz7UdN0WDjDTx5SekYBmcO_ULofXGwgsz95Yq6FhBQ%40mail.gmail.com?utm_medium=email&utm_source=footer>.
Belinda M. Giardine
Jan 2, 2024, 11:56:32 AM1/2/24
to Maximilian Haeussler, Hoover, David (NIH/CIT) [E], Mark Diekhans, Hiram Clawson, Christopher Lee, genome...@soe.ucsc.edu
We are building our own binaries. It is running on a VM.
Belinda
On Fri, 22 Dec 2023, Maximilian Haeussler wrote:
> David and Belinda,
> thank you for your patience with this, it's hard to debug if we don't have
> access to a machine and can't reproduce the problem. We don't think it's
> Rocky 9 itself (trying with a VM).
> Are you both building your own binaries from the source code or are you
> using our pre-built binaries?
> thanks
> Max
>
> On Mon, Dec 18, 2023 at 8:31?PM Belinda M. Giardine <giar...@bx.psu.edu>
>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov
>> .
>> .
>> .
>>
>
Belinda
On Fri, 22 Dec 2023, Maximilian Haeussler wrote:
> David and Belinda,
> thank you for your patience with this, it's hard to debug if we don't have
> access to a machine and can't reproduce the problem. We don't think it's
> Rocky 9 itself (trying with a VM).
> Are you both building your own binaries from the source code or are you
> using our pre-built binaries?
> thanks
> Max
>
>> .
>>>
>>> --
>>> David Hoover, Ph.D.
>>> Computational Biologist
>>> High Performance Computing Services,
>>> Center for Information Technology,
>>> National Institutes of Health
>>> 12 South Dr., Rm 2N207
>>> Bethesda, MD 20892, USA
>>> TEL: (+1) 301-435-2986
>>> Email: hoov...@hpc.nih.gov
>>>
>>> --
>>>
>>> --- You received this message because you are subscribed to the Google
>> Groups
>>> "UCSC Genome Browser Mirror-Specific Support" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>> an
>>> email to genome-mirro...@soe.ucsc.edu.
>>> To view this discussion on the web visit
>>>
>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov
>>> --
>>> David Hoover, Ph.D.
>>> Computational Biologist
>>> High Performance Computing Services,
>>> Center for Information Technology,
>>> National Institutes of Health
>>> 12 South Dr., Rm 2N207
>>> Bethesda, MD 20892, USA
>>> TEL: (+1) 301-435-2986
>>> Email: hoov...@hpc.nih.gov
>>>
>>> --
>>>
>>> --- You received this message because you are subscribed to the Google
>> Groups
>>> "UCSC Genome Browser Mirror-Specific Support" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>> an
>>> email to genome-mirro...@soe.ucsc.edu.
>>> To view this discussion on the web visit
>>>
>> .
>>>
>>>
>>
>> --
>>
>> ---
>> You received this message because you are subscribed to the Google Groups
>> "UCSC Genome Browser Mirror-Specific Support" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to genome-mirro...@soe.ucsc.edu.
>> To view this discussion on the web visit
>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu
>>>
>>
>> --
>>
>> ---
>> You received this message because you are subscribed to the Google Groups
>> "UCSC Genome Browser Mirror-Specific Support" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to genome-mirro...@soe.ucsc.edu.
>> To view this discussion on the web visit
>> .
>>
>
Jairo Navarro Gonzalez
Jan 16, 2024, 2:32:29 PM1/16/24
to Belinda M. Giardine, Maximilian Haeussler, Hoover, David (NIH/CIT) [E], Mark Diekhans, Hiram Clawson, Christopher Lee, genome...@soe.ucsc.edu
Hello,
Thank you for using the UCSC Genome Browser and reporting your issues.
Would it be possible to place the binaries in a web-accessible location? This way, our engineers can have a reproducible case to debug the issue.
If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Jairo Navarro
UCSC Genome Browser
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu.
Belinda M. Giardine
Jan 16, 2024, 3:15:02 PM1/16/24
to Jairo Navarro Gonzalez, Maximilian Haeussler, Hoover, David (NIH/CIT) [E], Mark Diekhans, Hiram Clawson, Christopher Lee, genome...@soe.ucsc.edu
I put a copy of the files in the cgi-bin here
https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/
If you mean you want to be able to access the pages on our server the
public version is
https://main.genome-browser.bx.psu.edu/
Belinda
On Tue, 16 Jan 2024, Jairo Navarro Gonzalez wrote:
> Hello,
>
> Thank you for using the UCSC Genome Browser and reporting your issues.
>
> Would it be possible to place the binaries in a web-accessible location?
> This way, our engineers can have a reproducible case to debug the issue.
>
> If you have any further questions, please reply to gen...@soe.ucsc.edu.
> All messages sent to that address are archived on a publicly accessible
> Google Groups forum.
> If your question includes sensitive data, you may send it instead to
> genom...@soe.ucsc.edu.
>
> Jairo Navarro
> UCSC Genome Browser
>
> On Tue, Jan 2, 2024 at 8:56?AM Belinda M. Giardine <giar...@bx.psu.edu>
https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/
If you mean you want to be able to access the pages on our server the
public version is
https://main.genome-browser.bx.psu.edu/
Belinda
On Tue, 16 Jan 2024, Jairo Navarro Gonzalez wrote:
> Hello,
>
> Thank you for using the UCSC Genome Browser and reporting your issues.
>
> Would it be possible to place the binaries in a web-accessible location?
> This way, our engineers can have a reproducible case to debug the issue.
>
> If you have any further questions, please reply to gen...@soe.ucsc.edu.
> All messages sent to that address are archived on a publicly accessible
> Google Groups forum.
> If your question includes sensitive data, you may send it instead to
> genom...@soe.ucsc.edu.
>
> Jairo Navarro
> UCSC Genome Browser
>
Christopher Lee
Jan 22, 2024, 2:44:48 PM1/22/24
to Belinda M. Giardine, Jairo Navarro Gonzalez, Maximilian Haeussler, Hoover, David (NIH/CIT) [E], Mark Diekhans, Hiram Clawson, genome...@soe.ucsc.edu
Hi Belinda and David,
Unfortunately we are just completely stumped on what is going on here,
and we do not have the resources to continue looking further. The only
thing we can say is that we ourselves are upgrading to Rocky 9 soon
and have verified at least minimal function with that operating
system, so you can try upgrading and see if that fixes the problem.
As far as theories, we suspect that somehow the MySQL/MariaDb
installation could be misconfigured, even though that seemed to have
been ruled out already.
If you do find the cause of the problem and/or a fix, we would of
course love to hear about it and accept a pull request or fix.
Thanks,
Christopher Lee
UCSC Genomics Institute
On Tue, Jan 16, 2024 at 12:07 PM Belinda M. Giardine
Unfortunately we are just completely stumped on what is going on here,
and we do not have the resources to continue looking further. The only
thing we can say is that we ourselves are upgrading to Rocky 9 soon
and have verified at least minimal function with that operating
system, so you can try upgrading and see if that fixes the problem.
As far as theories, we suspect that somehow the MySQL/MariaDb
installation could be misconfigured, even though that seemed to have
been ruled out already.
If you do find the cause of the problem and/or a fix, we would of
course love to hear about it and accept a pull request or fix.
Thanks,
Christopher Lee
UCSC Genomics Institute
On Tue, Jan 16, 2024 at 12:07 PM Belinda M. Giardine
Hoover, David (NIH/CIT) [E]
Jan 29, 2024, 12:45:18 PM1/29/24
to Christopher Lee, Belinda M. Giardine, Jairo Navarro Gonzalez, Maximilian Haeussler, Mark Diekhans, Hiram Clawson, genome...@soe.ucsc.edu
How up to date is the Docker procedure for the Genome Browser? How difficult would it be to create and use a docker image of the Genome Browser that does not have mysql running internally? We have a substantial mariadb server already full with UCSC data and constantly updated, as well as lots of users' custom tracks. The instructions at https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions are very generic and would need to be elaborated to accommodate our local mirror.
David
David
Maximilian Haeussler
Jan 29, 2024, 12:45:23 PM1/29/24
to Hoover, David (NIH/CIT) [E], Christopher Lee, Belinda M. Giardine, Jairo Navarro Gonzalez, Mark Diekhans, Hiram Clawson, genome...@soe.ucsc.edu
Hi David,
The docker procedure is current, I think. What do you mean with "generic"? The Unix commands are rather specific:
Can you elaborate what you mean with "accommodate our local mirror" ?
I wanted to try Rocky 8 next and unfortunately got distracted by grant reviews...
Hoover, David (NIH/CIT) [E]
Jan 29, 2024, 1:48:46 PM1/29/24
to Maximilian Haeussler, Christopher Lee, Belinda M. Giardine, Jairo Navarro Gonzalez, Mark Diekhans, Hiram Clawson, genome...@soe.ucsc.edu
By "generic", I mean just following the commands in the documentation without any deviation. MySQL is installed and run from within the docker container. We don't need this, as we already have a MariaDB server running locally.
We have a lot of users with custom tracks in our local MariaDB server, and so I hope the Docker version can maintain these. I believe it is possible to modify the hg.conf file within the Docker container after the fact, but I haven't gotten that far yet. The Docker image is quite large (~8GB), and so we've needed to create a large VM to handle it.
Does the browser installation procedure in the Dockerfile simply download pre-built executables, or does it compile anything?
David
On 1/29/2024 10:49 AM, 'Maximilian Haeussler' via UCSC Genome Browser Mirror-Specific Support wrote:
> Hi David,
> The docker procedure is current, I think. What do you mean with "generic"? The Unix commands are rather specific:
> https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions>
>
> How up to date is the Docker procedure for the Genome Browser? How difficult would it be to create and use a docker image of the Genome Browser that does not have mysql running internally? We have a substantial mariadb server already full with UCSC data and constantly updated, as well as lots of users' custom tracks. The instructions at https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions> are very generic and would need to be elaborated to accommodate our local mirror.
> >>>>>> genome.ucsc.edu <http://genome.ucsc.edu>
> >>>>>>>>>>> Genome Browser Mirror-Specific Support <genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu>
> >>>>>>>>>>>> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>
> To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com?utm_medium=email&utm_source=footer>.
We have a lot of users with custom tracks in our local MariaDB server, and so I hope the Docker version can maintain these. I believe it is possible to modify the hg.conf file within the Docker container after the fact, but I haven't gotten that far yet. The Docker image is quite large (~8GB), and so we've needed to create a large VM to handle it.
Does the browser installation procedure in the Dockerfile simply download pre-built executables, or does it compile anything?
David
On 1/29/2024 10:49 AM, 'Maximilian Haeussler' via UCSC Genome Browser Mirror-Specific Support wrote:
> Hi David,
> The docker procedure is current, I think. What do you mean with "generic"? The Unix commands are rather specific:
> Can you elaborate what you mean with "accommodate our local mirror" ?
>
> I just tried an Ubuntu 22 a few days ago and ran the browserSetup.sh script in it and it just worked. I didn't use the docker commands, ran the browserSetup.sh -b install manually but I had a working mirror 2 minutes later.
>
> I wanted to try Rocky 8 next and unfortunately got distracted by grant reviews...
>
>
>
> On Mon, Jan 29, 2024 at 3:38 PM Hoover, David (NIH/CIT) [E] <hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>> wrote:
>
> I just tried an Ubuntu 22 a few days ago and ran the browserSetup.sh script in it and it just worked. I didn't use the docker commands, ran the browserSetup.sh -b install manually but I had a working mirror 2 minutes later.
>
> I wanted to try Rocky 8 next and unfortunately got distracted by grant reviews...
>
>
>
>
> How up to date is the Docker procedure for the Genome Browser? How difficult would it be to create and use a docker image of the Genome Browser that does not have mysql running internally? We have a substantial mariadb server already full with UCSC data and constantly updated, as well as lots of users' custom tracks. The instructions at https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions> are very generic and would need to be elaborated to accommodate our local mirror.
>
> David
>
> On 1/22/2024 2:44 PM, Christopher Lee wrote:
> > Hi Belinda and David,
> >
> > Unfortunately we are just completely stumped on what is going on here,
> > and we do not have the resources to continue looking further. The only
> > thing we can say is that we ourselves are upgrading to Rocky 9 soon
> > and have verified at least minimal function with that operating
> > system, so you can try upgrading and see if that fixes the problem.
> >
> > As far as theories, we suspect that somehow the MySQL/MariaDb
> > installation could be misconfigured, even though that seemed to have
> > been ruled out already.
> >
> > If you do find the cause of the problem and/or a fix, we would of
> > course love to hear about it and accept a pull request or fix.
> >
> > Thanks,
> > Christopher Lee
> > UCSC Genomics Institute
> >
> > On Tue, Jan 16, 2024 at 12:07 PM Belinda M. Giardine
> > <giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>> wrote:
> >>
> >> I put a copy of the files in the cgi-bin here
> >> https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/ <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/>
> David
>
> On 1/22/2024 2:44 PM, Christopher Lee wrote:
> > Hi Belinda and David,
> >
> > Unfortunately we are just completely stumped on what is going on here,
> > and we do not have the resources to continue looking further. The only
> > thing we can say is that we ourselves are upgrading to Rocky 9 soon
> > and have verified at least minimal function with that operating
> > system, so you can try upgrading and see if that fixes the problem.
> >
> > As far as theories, we suspect that somehow the MySQL/MariaDb
> > installation could be misconfigured, even though that seemed to have
> > been ruled out already.
> >
> > If you do find the cause of the problem and/or a fix, we would of
> > course love to hear about it and accept a pull request or fix.
> >
> > Thanks,
> > Christopher Lee
> > UCSC Genomics Institute
> >
> > On Tue, Jan 16, 2024 at 12:07 PM Belinda M. Giardine
> > <giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>> wrote:
> >>
> >> I put a copy of the files in the cgi-bin here
> >>
> >> If you mean you want to be able to access the pages on our server the
> >> public version is
> >> https://main.genome-browser.bx.psu.edu/ <https://main.genome-browser.bx.psu.edu/>
> >> If you mean you want to be able to access the pages on our server the
> >> public version is
> >>
> >> Belinda
> >>
> >>
> >> On Tue, 16 Jan 2024, Jairo Navarro Gonzalez wrote:
> >>
> >>> Hello,
> >>>
> >>> Thank you for using the UCSC Genome Browser and reporting your issues.
> >>>
> >>> Would it be possible to place the binaries in a web-accessible location?
> >>> This way, our engineers can have a reproducible case to debug the issue.
> >>>
> >>> If you have any further questions, please reply to gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>.
> >> Belinda
> >>
> >>
> >> On Tue, 16 Jan 2024, Jairo Navarro Gonzalez wrote:
> >>
> >>> Hello,
> >>>
> >>> Thank you for using the UCSC Genome Browser and reporting your issues.
> >>>
> >>> Would it be possible to place the binaries in a web-accessible location?
> >>> This way, our engineers can have a reproducible case to debug the issue.
> >>>
> >>> All messages sent to that address are archived on a publicly accessible
> >>> Google Groups forum.
> >>> If your question includes sensitive data, you may send it instead to
> >>> genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>.
> >>> Google Groups forum.
> >>> If your question includes sensitive data, you may send it instead to
> >>>
> >>> Jairo Navarro
> >>> UCSC Genome Browser
> >>>
> >>> On Tue, Jan 2, 2024 at 8:56?AM Belinda M. Giardine <giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>>
> >>> Jairo Navarro
> >>> UCSC Genome Browser
> >>>
> >>> wrote:
> >>>
> >>>> We are building our own binaries. It is running on a VM.
> >>>>
> >>>> Belinda
> >>>>
> >>>>
> >>>> On Fri, 22 Dec 2023, Maximilian Haeussler wrote:
> >>>>
> >>>>> David and Belinda,
> >>>>> thank you for your patience with this, it's hard to debug if we don't
> >>>> have
> >>>>> access to a machine and can't reproduce the problem. We don't think it's
> >>>>> Rocky 9 itself (trying with a VM).
> >>>>> Are you both building your own binaries from the source code or are you
> >>>>> using our pre-built binaries?
> >>>>> thanks
> >>>>> Max
> >>>>>
> >>>>> On Mon, Dec 18, 2023 at 8:31?PM Belinda M. Giardine <giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>
> >>>
> >>>> We are building our own binaries. It is running on a VM.
> >>>>
> >>>> Belinda
> >>>>
> >>>>
> >>>> On Fri, 22 Dec 2023, Maximilian Haeussler wrote:
> >>>>
> >>>>> David and Belinda,
> >>>>> thank you for your patience with this, it's hard to debug if we don't
> >>>> have
> >>>>> access to a machine and can't reproduce the problem. We don't think it's
> >>>>> Rocky 9 itself (trying with a VM).
> >>>>> Are you both building your own binaries from the source code or are you
> >>>>> using our pre-built binaries?
> >>>>> thanks
> >>>>> Max
> >>>>>
> >>>>>
> >>>>>>>>>>> wrote:
> >>>>>>>>>>>>
> >>>>>>>>>>>> Now I am not so sure what is happening.? Here are some
> >>>> observations:
> >>>>>>>>>>>>
> >>>>>>>>>>>> * The timeout issue holds not just for custom tracks, for the
> >>>> track
> >>>>>>>>>>>> hubs as well
> >>>>>>>>>>>> * On the UCSC site, I can load tracks and a hub hosted on our
> >>>> local
> >>>>>>>>>>>> dataserver (hpc.nih.gov <http://hpc.nih.gov>), and these display normally
> >>>>>>>>>>> wrote:
> >>>>>>>>>>>>
> >>>>>>>>>>>> Now I am not so sure what is happening.? Here are some
> >>>> observations:
> >>>>>>>>>>>>
> >>>>>>>>>>>> * The timeout issue holds not just for custom tracks, for the
> >>>> track
> >>>>>>>>>>>> hubs as well
> >>>>>>>>>>>> * On the UCSC site, I can load tracks and a hub hosted on our
> >>>> local
> >>>>>>>>>>>>
> >>>>>>>>>>>> --
> >>>>>>>>>>>>
> >>>>>>>>>>>> ---
> >>>>>>>>>>>> You received this message because you are subscribed to the Google
> >>>>>>>>>>>> Groups "UCSC Genome Browser Mirror-Specific Support" group.
> >>>>>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
> >>>>>> send
> >>>>>>>>>>>> an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu>.
> >>>>>>>>>>>> --
> >>>>>>>>>>>>
> >>>>>>>>>>>> ---
> >>>>>>>>>>>> You received this message because you are subscribed to the Google
> >>>>>>>>>>>> Groups "UCSC Genome Browser Mirror-Specific Support" group.
> >>>>>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
> >>>>>> send
> >>>>>>>>>>>> To view this discussion on the web visit
> >>>>>>>>>>>>
> >>>>>>
> >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov>
> >>>>>>>>>>>>
> >>>>>>
> >>>>>> .
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> --
> >>>>>>>>> David Hoover, Ph.D.
> >>>>>>>>> Computational Biologist
> >>>>>>>>> High Performance Computing Services,
> >>>>>>>>> Center for Information Technology,
> >>>>>>>>> National Institutes of Health
> >>>>>>>>> 12 South Dr., Rm 2N207
> >>>>>>>>> Bethesda, MD 20892, USA
> >>>>>>>>> TEL: (+1) 301-435-2986
> >>>>>>>>> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> --
> >>>>>>>>> David Hoover, Ph.D.
> >>>>>>>>> Computational Biologist
> >>>>>>>>> High Performance Computing Services,
> >>>>>>>>> Center for Information Technology,
> >>>>>>>>> National Institutes of Health
> >>>>>>>>> 12 South Dr., Rm 2N207
> >>>>>>>>> Bethesda, MD 20892, USA
> >>>>>>>>> TEL: (+1) 301-435-2986
> >>>>>>>>>
> >>>>>>>>> --
> >>>>>>>>>
> >>>>>>>>> ---
> >>>>>>>>> You received this message because you are subscribed to the Google
> >>>>>> Groups
> >>>>>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> >>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
> >>>> send
> >>>>>> an
> >>>>>>>>> email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu>.
> >>>>>>>>> --
> >>>>>>>>>
> >>>>>>>>> ---
> >>>>>>>>> You received this message because you are subscribed to the Google
> >>>>>> Groups
> >>>>>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> >>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
> >>>> send
> >>>>>> an
> >>>>>>>>> To view this discussion on the web visit
> >>>>>>>>>
> >>>>>>
> >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov>
> >>>>>>>>>
> >>>>>>
> >>>>>> .
> >>>>>>>
> >>>>>>> --
> >>>>>>> David Hoover, Ph.D.
> >>>>>>> Computational Biologist
> >>>>>>> High Performance Computing Services,
> >>>>>>> Center for Information Technology,
> >>>>>>> National Institutes of Health
> >>>>>>> 12 South Dr., Rm 2N207
> >>>>>>> Bethesda, MD 20892, USA
> >>>>>>> TEL: (+1) 301-435-2986
> >>>>>>> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>
> >>>>>>>
> >>>>>>> --
> >>>>>>> David Hoover, Ph.D.
> >>>>>>> Computational Biologist
> >>>>>>> High Performance Computing Services,
> >>>>>>> Center for Information Technology,
> >>>>>>> National Institutes of Health
> >>>>>>> 12 South Dr., Rm 2N207
> >>>>>>> Bethesda, MD 20892, USA
> >>>>>>> TEL: (+1) 301-435-2986
> >>>>>>>
> >>>>>>> --
> >>>>>>>
> >>>>>>> --- You received this message because you are subscribed to the Google
> >>>>>> Groups
> >>>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> >>>>>>> To unsubscribe from this group and stop receiving emails from it, send
> >>>>>> an
> >>>>>>> email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu>.
> >>>>>>> --
> >>>>>>>
> >>>>>>> --- You received this message because you are subscribed to the Google
> >>>>>> Groups
> >>>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> >>>>>>> To unsubscribe from this group and stop receiving emails from it, send
> >>>>>> an
> >>>>>>> To view this discussion on the web visit
> >>>>>>>
> >>>>>>
> >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov>
> >>>>>>>
> >>>>>>
> >>>>>> .
> >>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>> --
> >>>>>>
> >>>>>> ---
> >>>>>> You received this message because you are subscribed to the Google
> >>>> Groups
> >>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> >>>>>> To unsubscribe from this group and stop receiving emails from it, send
> >>>> an
> >>>>>> email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu>.
> >>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>> --
> >>>>>>
> >>>>>> ---
> >>>>>> You received this message because you are subscribed to the Google
> >>>> Groups
> >>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> >>>>>> To unsubscribe from this group and stop receiving emails from it, send
> >>>> an
> >>>>>> To view this discussion on the web visit
> >>>>>>
> >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu>
> >>>>>>
> >>>>>> .
> >>>>>>
> >>>>>
> >>>>
> >>>> --
> >>>>
> >>>> ---
> >>>> You received this message because you are subscribed to the Google Groups
> >>>> "UCSC Genome Browser Mirror-Specific Support" group.
> >>>> To unsubscribe from this group and stop receiving emails from it, send an
> >>>> email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu>.
> >>>>>>
> >>>>>
> >>>>
> >>>> --
> >>>>
> >>>> ---
> >>>> You received this message because you are subscribed to the Google Groups
> >>>> "UCSC Genome Browser Mirror-Specific Support" group.
> >>>> To unsubscribe from this group and stop receiving emails from it, send an
> >>>> To view this discussion on the web visit
> >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu>
> >>>> .
> >>>>
> >>>
>
> --
> David Hoover, Ph.D.
> Computational Biologist
> High Performance Computing Services,
> Center for Information Technology,
> National Institutes of Health
> 12 South Dr., Rm 2N207
> Bethesda, MD 20892, USA
> TEL: (+1) 301-435-2986
> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>
> >>>>
> >>>
>
> --
> David Hoover, Ph.D.
> Computational Biologist
> High Performance Computing Services,
> Center for Information Technology,
> National Institutes of Health
> 12 South Dr., Rm 2N207
> Bethesda, MD 20892, USA
> TEL: (+1) 301-435-2986
>
> --
>
> ---
> You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirro...@soe.ucsc.edu>.
> --
>
> ---
> You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com?utm_medium=email&utm_source=footer>.
Maximilian Haeussler
Jan 30, 2024, 12:11:13 PM1/30/24
to Hoover, David (NIH/CIT) [E], Christopher Lee, Belinda M. Giardine, Jairo Navarro Gonzalez, Mark Diekhans, Hiram Clawson, genome...@soe.ucsc.edu
By "generic", I mean just following the commands in the documentation without any deviation. MySQL is installed and run from within the docker container. We don't need this, as we already have a MariaDB server running locally.
We have a lot of users with custom tracks in our local MariaDB server, and so I hope the Docker version can maintain these. I believe it is possible to modify the hg.conf file within the Docker container after the fact, but I haven't gotten that far yet.
Ah, I see what you mean: the dockerfile just downloads a basic Ubuntu, then runs "browserSetup.sh -b install". Nothing stops you from modifying the installation afterwards.
You can do the entire install yourself, either in a VM or empty docker container, you can run browserSetup.sh -b install manually (or use the Dockerfile), then point this browser to your own existing MySQL server in hg.conf. You should be able to remove the mysql files and even the mysql server from the docker container or VM afterwards.
The Docker image is quite large (~8GB), and so we've needed to create a large VM to handle it.
Hmm. The Docker image may be large compared to other docker images, but it's not large compared to what it has, it has mysql, apache, a copy of the hgcentral database, and lot of other things. Is it a problem to have a large docker container?
Does the browser installation procedure in the Dockerfile simply download pre-built executables, or does it compile anything?
Not yet, but I have been wanting to add an option to build locally for forever... let me try this today...
Maximilian Haeussler
Feb 5, 2024, 3:50:57 PM2/5/24
to Hoover, David (NIH/CIT) [E], Christopher Lee, Belinda M. Giardine, Jairo Navarro Gonzalez, Mark Diekhans, Hiram Clawson, genome...@soe.ucsc.edu
Hi David,
cp extTools.ra /usr/local/apache/cgi-bin
chmod g+w hgTracks
chmod a+rx hgTracks
rm -f /usr/local/apache/cgi-bin/hgTracks
mv hgTracks /usr/local/apache/cgi-bin/hgTracks
OK, I've spent time on this, but still can't reproduce it:
(1) Took an empty Rocky 8 VM on my laptop, installed and built the CGIs there, but can access hubs just fine. I'm not getting the error that you saw. I tried the Alfa hub, as this is also on the NIH campus:
https://ftp.ncbi.nlm.nih.gov/snp/population_frequency/TrackHub/latest/hub.txt. It displays without errors...
(2) So I added a command "dev" to our installation script. If you run this after the "mirror" command, it will install all requirements, clone the git repo and build all the CGIs from scratch. This should help you build the CGIs yourself in a fresh VM or Docker container and may also help us track down problems: you can now compare the (pretty simple) yum and make commands in that script with what you use. For example, there is no static linking with any dependencies if you look at the linker command (see below).
Here is the version of the script with the "dev" command, it will soon land on github but I am sending you a link right now so you can test it:
On a fresh VM or Docker container, you should be able to run these three commands to make a browser mirror and build everything:
sudo bash browserSetup.sh -b install
sudo bash browserSetup.sh dev
Linker command:
[root@rocky8 hgTracks]# make alpha
cc -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o hgTracks mainMain.o adjacencyTrack.o pubsTracks.o altGraphXTrack.o bamTrack.o barChartTrack.o bedGraph.o bedTrack.o bigBedTrack.o bigRmskTrack.o bigWarn.o bigWigTrack.o chainTrack.o cgapSageTrack.o chromGraphTrack.o config.o container.o contigTrack.o coverageTrack.o cytoBandTrack.o cutterTrack.o decorator.o expRatioTracks.o factorSource.o hgTracks.o interactTrack.o gencodeTracks.o goldTrack.o gtexTracks.o gtexEqtlClusterTrack.o gvfTrack.o halSnakeTrack.o lollyTrack.o longRangeTrack.o loweLabTracks.o lrgTrack.o mafTrack.o makeItemsTrack.o menu.o mouseOver.o multiWig.o netTrack.o peptideAtlasTrack.o pslTrack.o recTrackSets.o rmskJoinedTrack.o rmskTrack.o sampleTracks.o searchTracks.o simpleTracks.o snake.o sortWig.o switchGear.o transMapTracks.o wabaTrack.o wigTrack.o cds.o wigMafTrack.o encode.o variation.o vcfTrack.o transcriptome.o rnaFoldTrack.o retroGene.o hapmapTrack.o rnaPLFoldTrack.o wiki.o wikiTrack.o imageV2.o extTools.o hicTrack.o ../../lib/x86_64/jkhgapcgi.a ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a ../../lib/x86_64/optimalLeaf.a -lfreetype -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lm -lz -L/usr/lib64/mysql -lmysqlclient -lpthread -ldl -lssl -lcrypto -lresolv -lm -lrt -lstdc++ -lrtcp extTools.ra /usr/local/apache/cgi-bin
chmod g+w hgTracks
chmod a+rx hgTracks
rm -f /usr/local/apache/cgi-bin/hgTracks
mv hgTracks /usr/local/apache/cgi-bin/hgTracks
Hope this helps
Max
Maximilian Haeussler
Feb 6, 2024, 12:37:50 PM2/6/24
to Hoover, David (NIH/CIT) [E], Christopher Lee, Belinda M. Giardine, Jairo Navarro Gonzalez, Mark Diekhans, Hiram Clawson, genome...@soe.ucsc.edu
Hi David,
One of our hypotheses (Mark) was that the makefile may have picked up non-standard static libraries that exist on your servers. Yesterday, I checked on rocky8 that at least on a clean rocky8 that's not the case, but to reduce the possibility in the future, I've now changed common.mk and removed a lot of the hardcoded paths that are looking in various directories for static libraries (most of them outdated now).
The resulting binaries should use only dynamic libraries. If this change caused problems in your build, please let me know.
best
Max
Hoover, David (NIH/CIT) [E]
Feb 8, 2024, 1:10:27 PM2/8/24
to genome...@soe.ucsc.edu
Max,
Was the change to common.mk implemented in release v460? I will try recompiling on as generic a rocky8 host I can find.
David
On 2/6/2024 9:14 AM, 'Maximilian Haeussler' via UCSC Genome Browser Mirror-Specific Support wrote:
> Hi David,
>
> One of our hypotheses (Mark) was that the makefile may have picked up non-standard static libraries that exist on your servers. Yesterday, I checked on rocky8 that at least on a clean rocky8 that's not the case, but to reduce the possibility in the future, I've now changed common.mk <http://common.mk> and removed a lot of the hardcoded paths that are looking in various directories for static libraries (most of them outdated now).
> > https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions>>
> >
> > How up to date is the Docker procedure for the Genome Browser? How difficult would it be to create and use a docker image of the Genome Browser that does not have mysql running internally? We have a substantial mariadb server already full with UCSC data and constantly updated, as well as lots of users' custom tracks. The instructions at https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions>> are very generic and would need to be elaborated to accommodate our local mirror.
> > >>>>>> genome.ucsc.edu <http://genome.ucsc.edu> <http://genome.ucsc.edu <http://genome.ucsc.edu>>
> > >>>>>>>>>>> Genome Browser Mirror-Specific Support <genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu> <mailto:genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu>>
> > >>>>>>>>>>>> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>
> > To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com?utm_medium=email&utm_source=footer <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com?utm_medium=email&utm_source=footer>>.
Was the change to common.mk implemented in release v460? I will try recompiling on as generic a rocky8 host I can find.
David
On 2/6/2024 9:14 AM, 'Maximilian Haeussler' via UCSC Genome Browser Mirror-Specific Support wrote:
> Hi David,
>
> The resulting binaries should use only dynamic libraries. If this change caused problems in your build, please let me know.
>
> best
> Max
>
>
> best
> Max
>
> On Mon, Feb 5, 2024 at 5:22 PM Maximilian Haeussler <mhae...@ucsc.edu <mailto:mhae...@ucsc.edu>> wrote:
>
> Hi David,
>
> OK, I've spent time on this, but still can't reproduce it:
>
> (1) Took an empty Rocky 8 VM on my laptop, installed and built the CGIs there, but can access hubs just fine. I'm not getting the error that you saw. I tried the Alfa hub, as this is also on the NIH campus:
> https://ftp.ncbi.nlm.nih.gov/snp/population_frequency/TrackHub/latest/hub.txt <https://ftp.ncbi.nlm.nih.gov/snp/population_frequency/TrackHub/latest/hub.txt>. It displays without errors...
>
> Hi David,
>
> OK, I've spent time on this, but still can't reproduce it:
>
> (1) Took an empty Rocky 8 VM on my laptop, installed and built the CGIs there, but can access hubs just fine. I'm not getting the error that you saw. I tried the Alfa hub, as this is also on the NIH campus:
>
> (2) So I added a command "dev" to our installation script. If you run this after the "mirror" command, it will install all requirements, clone the git repo and build all the CGIs from scratch. This should help you build the CGIs yourself in a fresh VM or Docker container and may also help us track down problems: you can now compare the (pretty simple) yum and make commands in that script with what you use. For example, there is no static linking with any dependencies if you look at the linker command (see below).
> Here is the version of the script with the "dev" command, it will soon land on github but I am sending you a link right now so you can test it:
> https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh <https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh>
> (2) So I added a command "dev" to our installation script. If you run this after the "mirror" command, it will install all requirements, clone the git repo and build all the CGIs from scratch. This should help you build the CGIs yourself in a fresh VM or Docker container and may also help us track down problems: you can now compare the (pretty simple) yum and make commands in that script with what you use. For example, there is no static linking with any dependencies if you look at the linker command (see below).
> Here is the version of the script with the "dev" command, it will soon land on github but I am sending you a link right now so you can test it:
>
> On a fresh VM or Docker container, you should be able to run these three commands to make a browser mirror and build everything:
>
> wget https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh <https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh>
> On a fresh VM or Docker container, you should be able to run these three commands to make a browser mirror and build everything:
>
> > Can you elaborate what you mean with "accommodate our local mirror" ?
> >
> > I just tried an Ubuntu 22 a few days ago and ran the browserSetup.sh script in it and it just worked. I didn't use the docker commands, ran the browserSetup.sh -b install manually but I had a working mirror 2 minutes later.
> >
> > I wanted to try Rocky 8 next and unfortunately got distracted by grant reviews...
> >
> >
> >
> > On Mon, Jan 29, 2024 at 3:38 PM Hoover, David (NIH/CIT) [E] <hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>> wrote:
> >
> > I just tried an Ubuntu 22 a few days ago and ran the browserSetup.sh script in it and it just worked. I didn't use the docker commands, ran the browserSetup.sh -b install manually but I had a working mirror 2 minutes later.
> >
> > I wanted to try Rocky 8 next and unfortunately got distracted by grant reviews...
> >
> >
> >
> >
> > How up to date is the Docker procedure for the Genome Browser? How difficult would it be to create and use a docker image of the Genome Browser that does not have mysql running internally? We have a substantial mariadb server already full with UCSC data and constantly updated, as well as lots of users' custom tracks. The instructions at https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions>> are very generic and would need to be elaborated to accommodate our local mirror.
> >
> > David
> >
> > On 1/22/2024 2:44 PM, Christopher Lee wrote:
> > > Hi Belinda and David,
> > >
> > > Unfortunately we are just completely stumped on what is going on here,
> > > and we do not have the resources to continue looking further. The only
> > > thing we can say is that we ourselves are upgrading to Rocky 9 soon
> > > and have verified at least minimal function with that operating
> > > system, so you can try upgrading and see if that fixes the problem.
> > >
> > > As far as theories, we suspect that somehow the MySQL/MariaDb
> > > installation could be misconfigured, even though that seemed to have
> > > been ruled out already.
> > >
> > > If you do find the cause of the problem and/or a fix, we would of
> > > course love to hear about it and accept a pull request or fix.
> > >
> > > Thanks,
> > > Christopher Lee
> > > UCSC Genomics Institute
> > >
> > > On Tue, Jan 16, 2024 at 12:07 PM Belinda M. Giardine
> > David
> >
> > On 1/22/2024 2:44 PM, Christopher Lee wrote:
> > > Hi Belinda and David,
> > >
> > > Unfortunately we are just completely stumped on what is going on here,
> > > and we do not have the resources to continue looking further. The only
> > > thing we can say is that we ourselves are upgrading to Rocky 9 soon
> > > and have verified at least minimal function with that operating
> > > system, so you can try upgrading and see if that fixes the problem.
> > >
> > > As far as theories, we suspect that somehow the MySQL/MariaDb
> > > installation could be misconfigured, even though that seemed to have
> > > been ruled out already.
> > >
> > > If you do find the cause of the problem and/or a fix, we would of
> > > course love to hear about it and accept a pull request or fix.
> > >
> > > Thanks,
> > > Christopher Lee
> > > UCSC Genomics Institute
> > >
> > > On Tue, Jan 16, 2024 at 12:07 PM Belinda M. Giardine
> > > <giar...@bx.psu.edu <mailto:giar...@bx.psu.edu> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>>> wrote:
> > >>
> > >> I put a copy of the files in the cgi-bin here
> > >> https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/ <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/> <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/ <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/>>
> > >>
> > >> I put a copy of the files in the cgi-bin here
> > >>
> > >> If you mean you want to be able to access the pages on our server the
> > >> public version is
> > >> https://main.genome-browser.bx.psu.edu/ <https://main.genome-browser.bx.psu.edu/> <https://main.genome-browser.bx.psu.edu/ <https://main.genome-browser.bx.psu.edu/>>
> > >> If you mean you want to be able to access the pages on our server the
> > >> public version is
> > >>
> > >> Belinda
> > >>
> > >>
> > >> On Tue, 16 Jan 2024, Jairo Navarro Gonzalez wrote:
> > >>
> > >>> Hello,
> > >>>
> > >>> Thank you for using the UCSC Genome Browser and reporting your issues.
> > >>>
> > >>> Would it be possible to place the binaries in a web-accessible location?
> > >>> This way, our engineers can have a reproducible case to debug the issue.
> > >>>
> > >>> If you have any further questions, please reply to gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu> <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>>.
> > >> Belinda
> > >>
> > >>
> > >> On Tue, 16 Jan 2024, Jairo Navarro Gonzalez wrote:
> > >>
> > >>> Hello,
> > >>>
> > >>> Thank you for using the UCSC Genome Browser and reporting your issues.
> > >>>
> > >>> Would it be possible to place the binaries in a web-accessible location?
> > >>> This way, our engineers can have a reproducible case to debug the issue.
> > >>>
> > >>> All messages sent to that address are archived on a publicly accessible
> > >>> Google Groups forum.
> > >>> If your question includes sensitive data, you may send it instead to
> > >>> genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu> <mailto:genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>>.
> > >>> Google Groups forum.
> > >>> If your question includes sensitive data, you may send it instead to
> > >>>
> > >>> Jairo Navarro
> > >>> UCSC Genome Browser
> > >>>
> > >>> On Tue, Jan 2, 2024 at 8:56?AM Belinda M. Giardine <giar...@bx.psu.edu <mailto:giar...@bx.psu.edu> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>>>
> > >>> Jairo Navarro
> > >>> UCSC Genome Browser
> > >>>
> > >>> wrote:
> > >>>
> > >>>> We are building our own binaries. It is running on a VM.
> > >>>>
> > >>>> Belinda
> > >>>>
> > >>>>
> > >>>> On Fri, 22 Dec 2023, Maximilian Haeussler wrote:
> > >>>>
> > >>>>> David and Belinda,
> > >>>>> thank you for your patience with this, it's hard to debug if we don't
> > >>>> have
> > >>>>> access to a machine and can't reproduce the problem. We don't think it's
> > >>>>> Rocky 9 itself (trying with a VM).
> > >>>>> Are you both building your own binaries from the source code or are you
> > >>>>> using our pre-built binaries?
> > >>>>> thanks
> > >>>>> Max
> > >>>>>
> > >>>>> On Mon, Dec 18, 2023 at 8:31?PM Belinda M. Giardine <giar...@bx.psu.edu <mailto:giar...@bx.psu.edu> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>>
> > >>>
> > >>>> We are building our own binaries. It is running on a VM.
> > >>>>
> > >>>> Belinda
> > >>>>
> > >>>>
> > >>>> On Fri, 22 Dec 2023, Maximilian Haeussler wrote:
> > >>>>
> > >>>>> David and Belinda,
> > >>>>> thank you for your patience with this, it's hard to debug if we don't
> > >>>> have
> > >>>>> access to a machine and can't reproduce the problem. We don't think it's
> > >>>>> Rocky 9 itself (trying with a VM).
> > >>>>> Are you both building your own binaries from the source code or are you
> > >>>>> using our pre-built binaries?
> > >>>>> thanks
> > >>>>> Max
> > >>>>>
> > >>>>>
> > >>>>>>>>>>> wrote:
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> Now I am not so sure what is happening.? Here are some
> > >>>> observations:
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> * The timeout issue holds not just for custom tracks, for the
> > >>>> track
> > >>>>>>>>>>>> hubs as well
> > >>>>>>>>>>>> * On the UCSC site, I can load tracks and a hub hosted on our
> > >>>> local
> > >>>>>>>>>>>> dataserver (hpc.nih.gov <http://hpc.nih.gov> <http://hpc.nih.gov <http://hpc.nih.gov>>), and these display normally
> > >>>>>>>>>>> wrote:
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> Now I am not so sure what is happening.? Here are some
> > >>>> observations:
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> * The timeout issue holds not just for custom tracks, for the
> > >>>> track
> > >>>>>>>>>>>> hubs as well
> > >>>>>>>>>>>> * On the UCSC site, I can load tracks and a hub hosted on our
> > >>>> local
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> --
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> ---
> > >>>>>>>>>>>> You received this message because you are subscribed to the Google
> > >>>>>>>>>>>> Groups "UCSC Genome Browser Mirror-Specific Support" group.
> > >>>>>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
> > >>>>>> send
> > >>>>>>>>>>>> an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu>>.
> > >>>>>>>>>>>> --
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> ---
> > >>>>>>>>>>>> You received this message because you are subscribed to the Google
> > >>>>>>>>>>>> Groups "UCSC Genome Browser Mirror-Specific Support" group.
> > >>>>>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
> > >>>>>> send
> > >>>>>>>>>>>> To view this discussion on the web visit
> > >>>>>>>>>>>>
> > >>>>>>
> > >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov>>
> > >>>>>>>>>>>>
> > >>>>>>
> > >>>>>> .
> > >>>>>>>>>>>
> > >>>>>>>>>
> > >>>>>>>>> --
> > >>>>>>>>> David Hoover, Ph.D.
> > >>>>>>>>> Computational Biologist
> > >>>>>>>>> High Performance Computing Services,
> > >>>>>>>>> Center for Information Technology,
> > >>>>>>>>> National Institutes of Health
> > >>>>>>>>> 12 South Dr., Rm 2N207
> > >>>>>>>>> Bethesda, MD 20892, USA
> > >>>>>>>>> TEL: (+1) 301-435-2986
> > >>>>>>>>> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>
> > >>>>>>>>>>>
> > >>>>>>>>>
> > >>>>>>>>> --
> > >>>>>>>>> David Hoover, Ph.D.
> > >>>>>>>>> Computational Biologist
> > >>>>>>>>> High Performance Computing Services,
> > >>>>>>>>> Center for Information Technology,
> > >>>>>>>>> National Institutes of Health
> > >>>>>>>>> 12 South Dr., Rm 2N207
> > >>>>>>>>> Bethesda, MD 20892, USA
> > >>>>>>>>> TEL: (+1) 301-435-2986
> > >>>>>>>>>
> > >>>>>>>>> --
> > >>>>>>>>>
> > >>>>>>>>> ---
> > >>>>>>>>> You received this message because you are subscribed to the Google
> > >>>>>> Groups
> > >>>>>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > >>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
> > >>>> send
> > >>>>>> an
> > >>>>>>>>> email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu>>.
> > >>>>>>>>> --
> > >>>>>>>>>
> > >>>>>>>>> ---
> > >>>>>>>>> You received this message because you are subscribed to the Google
> > >>>>>> Groups
> > >>>>>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > >>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
> > >>>> send
> > >>>>>> an
> > >>>>>>>>> To view this discussion on the web visit
> > >>>>>>>>>
> > >>>>>>
> > >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov>>
> > >>>>>>>>>
> > >>>>>>
> > >>>>>> .
> > >>>>>>>
> > >>>>>>> --
> > >>>>>>> David Hoover, Ph.D.
> > >>>>>>> Computational Biologist
> > >>>>>>> High Performance Computing Services,
> > >>>>>>> Center for Information Technology,
> > >>>>>>> National Institutes of Health
> > >>>>>>> 12 South Dr., Rm 2N207
> > >>>>>>> Bethesda, MD 20892, USA
> > >>>>>>> TEL: (+1) 301-435-2986
> > >>>>>>> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>
> > >>>>>>>
> > >>>>>>> --
> > >>>>>>> David Hoover, Ph.D.
> > >>>>>>> Computational Biologist
> > >>>>>>> High Performance Computing Services,
> > >>>>>>> Center for Information Technology,
> > >>>>>>> National Institutes of Health
> > >>>>>>> 12 South Dr., Rm 2N207
> > >>>>>>> Bethesda, MD 20892, USA
> > >>>>>>> TEL: (+1) 301-435-2986
> > >>>>>>>
> > >>>>>>> --
> > >>>>>>>
> > >>>>>>> --- You received this message because you are subscribed to the Google
> > >>>>>> Groups
> > >>>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > >>>>>>> To unsubscribe from this group and stop receiving emails from it, send
> > >>>>>> an
> > >>>>>>> email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu>>.
> > >>>>>>> --
> > >>>>>>>
> > >>>>>>> --- You received this message because you are subscribed to the Google
> > >>>>>> Groups
> > >>>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > >>>>>>> To unsubscribe from this group and stop receiving emails from it, send
> > >>>>>> an
> > >>>>>>> To view this discussion on the web visit
> > >>>>>>>
> > >>>>>>
> > >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov>>
> > >>>>>>>
> > >>>>>>
> > >>>>>> .
> > >>>>>>>
> > >>>>>>>
> > >>>>>>
> > >>>>>> --
> > >>>>>>
> > >>>>>> ---
> > >>>>>> You received this message because you are subscribed to the Google
> > >>>> Groups
> > >>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > >>>>>> To unsubscribe from this group and stop receiving emails from it, send
> > >>>> an
> > >>>>>> email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu>>.
> > >>>>>>>
> > >>>>>>>
> > >>>>>>
> > >>>>>> --
> > >>>>>>
> > >>>>>> ---
> > >>>>>> You received this message because you are subscribed to the Google
> > >>>> Groups
> > >>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > >>>>>> To unsubscribe from this group and stop receiving emails from it, send
> > >>>> an
> > >>>>>> To view this discussion on the web visit
> > >>>>>>
> > >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu>>
> > >>>>>>
> > >>>>>> .
> > >>>>>>
> > >>>>>
> > >>>>
> > >>>> --
> > >>>>
> > >>>> ---
> > >>>> You received this message because you are subscribed to the Google Groups
> > >>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > >>>> To unsubscribe from this group and stop receiving emails from it, send an
> > >>>> email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu>>.
> > >>>>>>
> > >>>>>
> > >>>>
> > >>>> --
> > >>>>
> > >>>> ---
> > >>>> You received this message because you are subscribed to the Google Groups
> > >>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > >>>> To unsubscribe from this group and stop receiving emails from it, send an
> > >>>> To view this discussion on the web visit
> > >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu>>
> > >>>> .
> > >>>>
> > >>>
> >
> > --
> > David Hoover, Ph.D.
> > Computational Biologist
> > High Performance Computing Services,
> > Center for Information Technology,
> > National Institutes of Health
> > 12 South Dr., Rm 2N207
> > Bethesda, MD 20892, USA
> > TEL: (+1) 301-435-2986
> > Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>
> > >>>>
> > >>>
> >
> > --
> > David Hoover, Ph.D.
> > Computational Biologist
> > High Performance Computing Services,
> > Center for Information Technology,
> > National Institutes of Health
> > 12 South Dr., Rm 2N207
> > Bethesda, MD 20892, USA
> > TEL: (+1) 301-435-2986
> >
> > --
> >
> > ---
> > You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> > To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu>>.
> > --
> >
> > ---
> > You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> > To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com?utm_medium=email&utm_source=footer <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com?utm_medium=email&utm_source=footer>>.
>
> --
> David Hoover, Ph.D.
> Computational Biologist
> High Performance Computing Services,
> Center for Information Technology,
> National Institutes of Health
> 12 South Dr., Rm 2N207
> Bethesda, MD 20892, USA
> TEL: (+1) 301-435-2986
> --
> David Hoover, Ph.D.
> Computational Biologist
> High Performance Computing Services,
> Center for Information Technology,
> National Institutes of Health
> 12 South Dr., Rm 2N207
> Bethesda, MD 20892, USA
> TEL: (+1) 301-435-2986
> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>
>
> --
>
> ---
> You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirro...@soe.ucsc.edu>.
> To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fwTvVmGRacUWg9P2goKjCedNfWo0DTNYd0_GaGCBHtFdg%40mail.gmail.com <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fwTvVmGRacUWg9P2goKjCedNfWo0DTNYd0_GaGCBHtFdg%40mail.gmail.com?utm_medium=email&utm_source=footer>.
>
> --
>
> ---
> You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirro...@soe.ucsc.edu>.
Hoover, David (NIH/CIT) [E]
Feb 9, 2024, 12:46:11 PM2/9/24
to genome...@soe.ucsc.edu
When you run the Genome Browser under rocky8, do you have selinux enabled?
David
On 2/5/2024 11:22 AM, 'Maximilian Haeussler' via UCSC Genome Browser Mirror-Specific Support wrote:
> Hi David,
>
> > https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions>>
> >
> > How up to date is the Docker procedure for the Genome Browser? How difficult would it be to create and use a docker image of the Genome Browser that does not have mysql running internally? We have a substantial mariadb server already full with UCSC data and constantly updated, as well as lots of users' custom tracks. The instructions at https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions>> are very generic and would need to be elaborated to accommodate our local mirror.
> > >>>>>> genome.ucsc.edu <http://genome.ucsc.edu> <http://genome.ucsc.edu <http://genome.ucsc.edu>>
> > >>>>>>>>>>> Genome Browser Mirror-Specific Support <genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu> <mailto:genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu>>
> > >>>>>>>>>>>> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>
David
On 2/5/2024 11:22 AM, 'Maximilian Haeussler' via UCSC Genome Browser Mirror-Specific Support wrote:
> Hi David,
>
> OK, I've spent time on this, but still can't reproduce it:
>
> (1) Took an empty Rocky 8 VM on my laptop, installed and built the CGIs there, but can access hubs just fine. I'm not getting the error that you saw. I tried the Alfa hub, as this is also on the NIH campus:
> https://ftp.ncbi.nlm.nih.gov/snp/population_frequency/TrackHub/latest/hub.txt <https://ftp.ncbi.nlm.nih.gov/snp/population_frequency/TrackHub/latest/hub.txt>. It displays without errors...
>
> (1) Took an empty Rocky 8 VM on my laptop, installed and built the CGIs there, but can access hubs just fine. I'm not getting the error that you saw. I tried the Alfa hub, as this is also on the NIH campus:
>
> (2) So I added a command "dev" to our installation script. If you run this after the "mirror" command, it will install all requirements, clone the git repo and build all the CGIs from scratch. This should help you build the CGIs yourself in a fresh VM or Docker container and may also help us track down problems: you can now compare the (pretty simple) yum and make commands in that script with what you use. For example, there is no static linking with any dependencies if you look at the linker command (see below).
> Here is the version of the script with the "dev" command, it will soon land on github but I am sending you a link right now so you can test it:
> https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh <https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh>
> (2) So I added a command "dev" to our installation script. If you run this after the "mirror" command, it will install all requirements, clone the git repo and build all the CGIs from scratch. This should help you build the CGIs yourself in a fresh VM or Docker container and may also help us track down problems: you can now compare the (pretty simple) yum and make commands in that script with what you use. For example, there is no static linking with any dependencies if you look at the linker command (see below).
> Here is the version of the script with the "dev" command, it will soon land on github but I am sending you a link right now so you can test it:
>
> On a fresh VM or Docker container, you should be able to run these three commands to make a browser mirror and build everything:
>
> wget https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh <https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh>
> On a fresh VM or Docker container, you should be able to run these three commands to make a browser mirror and build everything:
>
> > Can you elaborate what you mean with "accommodate our local mirror" ?
> >
> > I just tried an Ubuntu 22 a few days ago and ran the browserSetup.sh script in it and it just worked. I didn't use the docker commands, ran the browserSetup.sh -b install manually but I had a working mirror 2 minutes later.
> >
> > I wanted to try Rocky 8 next and unfortunately got distracted by grant reviews...
> >
> >
> >
> > On Mon, Jan 29, 2024 at 3:38 PM Hoover, David (NIH/CIT) [E] <hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>> wrote:
> >
> > I just tried an Ubuntu 22 a few days ago and ran the browserSetup.sh script in it and it just worked. I didn't use the docker commands, ran the browserSetup.sh -b install manually but I had a working mirror 2 minutes later.
> >
> > I wanted to try Rocky 8 next and unfortunately got distracted by grant reviews...
> >
> >
> >
> >
> > How up to date is the Docker procedure for the Genome Browser? How difficult would it be to create and use a docker image of the Genome Browser that does not have mysql running internally? We have a substantial mariadb server already full with UCSC data and constantly updated, as well as lots of users' custom tracks. The instructions at https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions>> are very generic and would need to be elaborated to accommodate our local mirror.
> >
> > David
> >
> > On 1/22/2024 2:44 PM, Christopher Lee wrote:
> > > Hi Belinda and David,
> > >
> > > Unfortunately we are just completely stumped on what is going on here,
> > > and we do not have the resources to continue looking further. The only
> > > thing we can say is that we ourselves are upgrading to Rocky 9 soon
> > > and have verified at least minimal function with that operating
> > > system, so you can try upgrading and see if that fixes the problem.
> > >
> > > As far as theories, we suspect that somehow the MySQL/MariaDb
> > > installation could be misconfigured, even though that seemed to have
> > > been ruled out already.
> > >
> > > If you do find the cause of the problem and/or a fix, we would of
> > > course love to hear about it and accept a pull request or fix.
> > >
> > > Thanks,
> > > Christopher Lee
> > > UCSC Genomics Institute
> > >
> > > On Tue, Jan 16, 2024 at 12:07 PM Belinda M. Giardine
> > David
> >
> > On 1/22/2024 2:44 PM, Christopher Lee wrote:
> > > Hi Belinda and David,
> > >
> > > Unfortunately we are just completely stumped on what is going on here,
> > > and we do not have the resources to continue looking further. The only
> > > thing we can say is that we ourselves are upgrading to Rocky 9 soon
> > > and have verified at least minimal function with that operating
> > > system, so you can try upgrading and see if that fixes the problem.
> > >
> > > As far as theories, we suspect that somehow the MySQL/MariaDb
> > > installation could be misconfigured, even though that seemed to have
> > > been ruled out already.
> > >
> > > If you do find the cause of the problem and/or a fix, we would of
> > > course love to hear about it and accept a pull request or fix.
> > >
> > > Thanks,
> > > Christopher Lee
> > > UCSC Genomics Institute
> > >
> > > On Tue, Jan 16, 2024 at 12:07 PM Belinda M. Giardine
> > > <giar...@bx.psu.edu <mailto:giar...@bx.psu.edu> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>>> wrote:
> > >>
> > >> I put a copy of the files in the cgi-bin here
> > >> https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/ <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/> <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/ <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/>>
> > >>
> > >> I put a copy of the files in the cgi-bin here
> > >>
> > >> If you mean you want to be able to access the pages on our server the
> > >> public version is
> > >> https://main.genome-browser.bx.psu.edu/ <https://main.genome-browser.bx.psu.edu/> <https://main.genome-browser.bx.psu.edu/ <https://main.genome-browser.bx.psu.edu/>>
> > >> If you mean you want to be able to access the pages on our server the
> > >> public version is
> > >>
> > >> Belinda
> > >>
> > >>
> > >> On Tue, 16 Jan 2024, Jairo Navarro Gonzalez wrote:
> > >>
> > >>> Hello,
> > >>>
> > >>> Thank you for using the UCSC Genome Browser and reporting your issues.
> > >>>
> > >>> Would it be possible to place the binaries in a web-accessible location?
> > >>> This way, our engineers can have a reproducible case to debug the issue.
> > >>>
> > >>> If you have any further questions, please reply to gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu> <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>>.
> > >> Belinda
> > >>
> > >>
> > >> On Tue, 16 Jan 2024, Jairo Navarro Gonzalez wrote:
> > >>
> > >>> Hello,
> > >>>
> > >>> Thank you for using the UCSC Genome Browser and reporting your issues.
> > >>>
> > >>> Would it be possible to place the binaries in a web-accessible location?
> > >>> This way, our engineers can have a reproducible case to debug the issue.
> > >>>
> > >>> All messages sent to that address are archived on a publicly accessible
> > >>> Google Groups forum.
> > >>> If your question includes sensitive data, you may send it instead to
> > >>> genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu> <mailto:genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>>.
> > >>> Google Groups forum.
> > >>> If your question includes sensitive data, you may send it instead to
> > >>>
> > >>> Jairo Navarro
> > >>> UCSC Genome Browser
> > >>>
> > >>> On Tue, Jan 2, 2024 at 8:56?AM Belinda M. Giardine <giar...@bx.psu.edu <mailto:giar...@bx.psu.edu> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>>>
> > >>> Jairo Navarro
> > >>> UCSC Genome Browser
> > >>>
> > >>> wrote:
> > >>>
> > >>>> We are building our own binaries. It is running on a VM.
> > >>>>
> > >>>> Belinda
> > >>>>
> > >>>>
> > >>>> On Fri, 22 Dec 2023, Maximilian Haeussler wrote:
> > >>>>
> > >>>>> David and Belinda,
> > >>>>> thank you for your patience with this, it's hard to debug if we don't
> > >>>> have
> > >>>>> access to a machine and can't reproduce the problem. We don't think it's
> > >>>>> Rocky 9 itself (trying with a VM).
> > >>>>> Are you both building your own binaries from the source code or are you
> > >>>>> using our pre-built binaries?
> > >>>>> thanks
> > >>>>> Max
> > >>>>>
> > >>>>> On Mon, Dec 18, 2023 at 8:31?PM Belinda M. Giardine <giar...@bx.psu.edu <mailto:giar...@bx.psu.edu> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>>
> > >>>
> > >>>> We are building our own binaries. It is running on a VM.
> > >>>>
> > >>>> Belinda
> > >>>>
> > >>>>
> > >>>> On Fri, 22 Dec 2023, Maximilian Haeussler wrote:
> > >>>>
> > >>>>> David and Belinda,
> > >>>>> thank you for your patience with this, it's hard to debug if we don't
> > >>>> have
> > >>>>> access to a machine and can't reproduce the problem. We don't think it's
> > >>>>> Rocky 9 itself (trying with a VM).
> > >>>>> Are you both building your own binaries from the source code or are you
> > >>>>> using our pre-built binaries?
> > >>>>> thanks
> > >>>>> Max
> > >>>>>
> > >>>>>
> > >>>>>>>>>>> wrote:
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> Now I am not so sure what is happening.? Here are some
> > >>>> observations:
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> * The timeout issue holds not just for custom tracks, for the
> > >>>> track
> > >>>>>>>>>>>> hubs as well
> > >>>>>>>>>>>> * On the UCSC site, I can load tracks and a hub hosted on our
> > >>>> local
> > >>>>>>>>>>>> dataserver (hpc.nih.gov <http://hpc.nih.gov> <http://hpc.nih.gov <http://hpc.nih.gov>>), and these display normally
> > >>>>>>>>>>> wrote:
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> Now I am not so sure what is happening.? Here are some
> > >>>> observations:
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> * The timeout issue holds not just for custom tracks, for the
> > >>>> track
> > >>>>>>>>>>>> hubs as well
> > >>>>>>>>>>>> * On the UCSC site, I can load tracks and a hub hosted on our
> > >>>> local
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> --
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> ---
> > >>>>>>>>>>>> You received this message because you are subscribed to the Google
> > >>>>>>>>>>>> Groups "UCSC Genome Browser Mirror-Specific Support" group.
> > >>>>>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
> > >>>>>> send
> > >>>>>>>>>>>> an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu>>.
> > >>>>>>>>>>>> --
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> ---
> > >>>>>>>>>>>> You received this message because you are subscribed to the Google
> > >>>>>>>>>>>> Groups "UCSC Genome Browser Mirror-Specific Support" group.
> > >>>>>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
> > >>>>>> send
> > >>>>>>>>>>>> To view this discussion on the web visit
> > >>>>>>>>>>>>
> > >>>>>>
> > >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov>>
> > >>>>>>>>>>>>
> > >>>>>>
> > >>>>>> .
> > >>>>>>>>>>>
> > >>>>>>>>>
> > >>>>>>>>> --
> > >>>>>>>>> David Hoover, Ph.D.
> > >>>>>>>>> Computational Biologist
> > >>>>>>>>> High Performance Computing Services,
> > >>>>>>>>> Center for Information Technology,
> > >>>>>>>>> National Institutes of Health
> > >>>>>>>>> 12 South Dr., Rm 2N207
> > >>>>>>>>> Bethesda, MD 20892, USA
> > >>>>>>>>> TEL: (+1) 301-435-2986
> > >>>>>>>>> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>
> > >>>>>>>>>>>
> > >>>>>>>>>
> > >>>>>>>>> --
> > >>>>>>>>> David Hoover, Ph.D.
> > >>>>>>>>> Computational Biologist
> > >>>>>>>>> High Performance Computing Services,
> > >>>>>>>>> Center for Information Technology,
> > >>>>>>>>> National Institutes of Health
> > >>>>>>>>> 12 South Dr., Rm 2N207
> > >>>>>>>>> Bethesda, MD 20892, USA
> > >>>>>>>>> TEL: (+1) 301-435-2986
> > >>>>>>>>>
> > >>>>>>>>> --
> > >>>>>>>>>
> > >>>>>>>>> ---
> > >>>>>>>>> You received this message because you are subscribed to the Google
> > >>>>>> Groups
> > >>>>>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > >>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
> > >>>> send
> > >>>>>> an
> > >>>>>>>>> email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu>>.
> > >>>>>>>>> --
> > >>>>>>>>>
> > >>>>>>>>> ---
> > >>>>>>>>> You received this message because you are subscribed to the Google
> > >>>>>> Groups
> > >>>>>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > >>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
> > >>>> send
> > >>>>>> an
> > >>>>>>>>> To view this discussion on the web visit
> > >>>>>>>>>
> > >>>>>>
> > >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov>>
> > >>>>>>>>>
> > >>>>>>
> > >>>>>> .
> > >>>>>>>
> > >>>>>>> --
> > >>>>>>> David Hoover, Ph.D.
> > >>>>>>> Computational Biologist
> > >>>>>>> High Performance Computing Services,
> > >>>>>>> Center for Information Technology,
> > >>>>>>> National Institutes of Health
> > >>>>>>> 12 South Dr., Rm 2N207
> > >>>>>>> Bethesda, MD 20892, USA
> > >>>>>>> TEL: (+1) 301-435-2986
> > >>>>>>> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>
> > >>>>>>>
> > >>>>>>> --
> > >>>>>>> David Hoover, Ph.D.
> > >>>>>>> Computational Biologist
> > >>>>>>> High Performance Computing Services,
> > >>>>>>> Center for Information Technology,
> > >>>>>>> National Institutes of Health
> > >>>>>>> 12 South Dr., Rm 2N207
> > >>>>>>> Bethesda, MD 20892, USA
> > >>>>>>> TEL: (+1) 301-435-2986
> > >>>>>>>
> > >>>>>>> --
> > >>>>>>>
> > >>>>>>> --- You received this message because you are subscribed to the Google
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> > >>>>>>> --
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> > >>>>>>>
> > >>>>>>
> > >>>>>> .
> > >>>>>>>
> > >>>>>>>
> > >>>>>>
> > >>>>>> --
> > >>>>>>
> > >>>>>> ---
> > >>>>>> You received this message because you are subscribed to the Google
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> > >>>>>>>
> > >>>>>>>
> > >>>>>>
> > >>>>>> --
> > >>>>>>
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> > >>>>>> You received this message because you are subscribed to the Google
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> > >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu>>
> > >>>>>>
> > >>>>>> .
> > >>>>>>
> > >>>>>
> > >>>>
> > >>>> --
> > >>>>
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> > >>>>>>
> > >>>>>
> > >>>>
> > >>>> --
> > >>>>
> > >>>> ---
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> > >>>> .
> > >>>>
> > >>>
> >
> > --
> > David Hoover, Ph.D.
> > Computational Biologist
> > High Performance Computing Services,
> > Center for Information Technology,
> > National Institutes of Health
> > 12 South Dr., Rm 2N207
> > Bethesda, MD 20892, USA
> > TEL: (+1) 301-435-2986
> > Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>
> > >>>>
> > >>>
> >
> > --
> > David Hoover, Ph.D.
> > Computational Biologist
> > High Performance Computing Services,
> > Center for Information Technology,
> > National Institutes of Health
> > 12 South Dr., Rm 2N207
> > Bethesda, MD 20892, USA
> > TEL: (+1) 301-435-2986
> >
> > --
> >
> > ---
> > You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> > --
> >
> > ---
> > You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> > To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu>>.
> > To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com?utm_medium=email&utm_source=footer <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com?utm_medium=email&utm_source=footer>>.
>
> --
> David Hoover, Ph.D.
> Computational Biologist
> High Performance Computing Services,
> Center for Information Technology,
> National Institutes of Health
> 12 South Dr., Rm 2N207
> Bethesda, MD 20892, USA
> TEL: (+1) 301-435-2986
> --
> David Hoover, Ph.D.
> Computational Biologist
> High Performance Computing Services,
> Center for Information Technology,
> National Institutes of Health
> 12 South Dr., Rm 2N207
> Bethesda, MD 20892, USA
> TEL: (+1) 301-435-2986
> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>
>
> --
>
> ---
> You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirro...@soe.ucsc.edu>.
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>
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> ---
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Maximilian Haeussler
Feb 9, 2024, 4:31:25 PM2/9/24
to Hoover, David (NIH/CIT) [E], genome...@soe.ucsc.edu
The script should have switched off selinux, did that not work?
To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/4873e9c1-f343-801b-5067-ee805a140150%40hpc.nih.gov.
Hoover, David (NIH/CIT) [E]
Feb 12, 2024, 1:32:02 PM2/12/24
to genome...@soe.ucsc.edu
Max,
I've gotten the docker version of the Genome Browser up and running. I managed to edit hg.conf so that it uses our local mariadb server. I can create custom tracks and everything works well.
However, one thing that is still broken. When I attempt to log into my local GB account using the hgLogin executable, it authenticates but then immediately signs me out. Do you have any idea what might be going wrong?
Here are my changes to hg.conf:
wiki.userNameCookie=wikidb_mw1_UserName
wiki.loggedInCookie=wikidb_mw1_UserID
wiki.host=HTTPHOST
login.systemName=UCSC Genome Browser Mirror
login.browserName=Helix Systems Genome Browser
login.browserAddr=10.1.201.160:8080/
login.mailSignature=Helix Systems Staff
login.mailReturnAddr=webt...@helix.nih.gov
David
On 2/9/2024 12:56 PM, 'Maximilian Haeussler' via UCSC Genome Browser Mirror-Specific Support wrote:
> The script should have switched off selinux, did that not work?
>
> > > https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions>> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions>>>
> > >
> > > How up to date is the Docker procedure for the Genome Browser? How difficult would it be to create and use a docker image of the Genome Browser that does not have mysql running internally? We have a substantial mariadb server already full with UCSC data and constantly updated, as well as lots of users' custom tracks. The instructions at https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions>> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions
> > > >>>>>> genome.ucsc.edu <http://genome.ucsc.edu> <http://genome.ucsc.edu <http://genome.ucsc.edu>> <http://genome.ucsc.edu <http://genome.ucsc.edu> <http://genome.ucsc.edu <http://genome.ucsc.edu>>>
> > > >>>>>>>>>>> Genome Browser Mirror-Specific Support <genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu> <mailto:genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu>> <mailto:genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu> <mailto:genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu>>>
> > > >>>>>>>>>>>> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>>
> > > To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com?utm_medium=email&utm_source=footer <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com?utm_medium=email&utm_source=footer>
> To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/4873e9c1-f343-801b-5067-ee805a140150%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/4873e9c1-f343-801b-5067-ee805a140150%40hpc.nih.gov>.
I've gotten the docker version of the Genome Browser up and running. I managed to edit hg.conf so that it uses our local mariadb server. I can create custom tracks and everything works well.
However, one thing that is still broken. When I attempt to log into my local GB account using the hgLogin executable, it authenticates but then immediately signs me out. Do you have any idea what might be going wrong?
Here are my changes to hg.conf:
wiki.userNameCookie=wikidb_mw1_UserName
wiki.loggedInCookie=wikidb_mw1_UserID
wiki.host=HTTPHOST
login.systemName=UCSC Genome Browser Mirror
login.browserName=Helix Systems Genome Browser
login.browserAddr=10.1.201.160:8080/
login.mailSignature=Helix Systems Staff
login.mailReturnAddr=webt...@helix.nih.gov
David
On 2/9/2024 12:56 PM, 'Maximilian Haeussler' via UCSC Genome Browser Mirror-Specific Support wrote:
> The script should have switched off selinux, did that not work?
>
> On Fri, Feb 9, 2024 at 6:46 PM 'Hoover, David (NIH/CIT) [E]' via UCSC Genome Browser Mirror-Specific Support <genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu>> wrote:
>
> When you run the Genome Browser under rocky8, do you have selinux enabled?
>
> David
>
> On 2/5/2024 11:22 AM, 'Maximilian Haeussler' via UCSC Genome Browser Mirror-Specific Support wrote:
> > Hi David,
> >
> > OK, I've spent time on this, but still can't reproduce it:
> >
> > (1) Took an empty Rocky 8 VM on my laptop, installed and built the CGIs there, but can access hubs just fine. I'm not getting the error that you saw. I tried the Alfa hub, as this is also on the NIH campus:
> > https://ftp.ncbi.nlm.nih.gov/snp/population_frequency/TrackHub/latest/hub.txt <https://ftp.ncbi.nlm.nih.gov/snp/population_frequency/TrackHub/latest/hub.txt> <https://ftp.ncbi.nlm.nih.gov/snp/population_frequency/TrackHub/latest/hub.txt <https://ftp.ncbi.nlm.nih.gov/snp/population_frequency/TrackHub/latest/hub.txt>>. It displays without errors...
>
> When you run the Genome Browser under rocky8, do you have selinux enabled?
>
> David
>
> On 2/5/2024 11:22 AM, 'Maximilian Haeussler' via UCSC Genome Browser Mirror-Specific Support wrote:
> > Hi David,
> >
> > OK, I've spent time on this, but still can't reproduce it:
> >
> > (1) Took an empty Rocky 8 VM on my laptop, installed and built the CGIs there, but can access hubs just fine. I'm not getting the error that you saw. I tried the Alfa hub, as this is also on the NIH campus:
> >
> > (2) So I added a command "dev" to our installation script. If you run this after the "mirror" command, it will install all requirements, clone the git repo and build all the CGIs from scratch. This should help you build the CGIs yourself in a fresh VM or Docker container and may also help us track down problems: you can now compare the (pretty simple) yum and make commands in that script with what you use. For example, there is no static linking with any dependencies if you look at the linker command (see below).
> > Here is the version of the script with the "dev" command, it will soon land on github but I am sending you a link right now so you can test it:
> > https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh <https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh> <https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh <https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh>>
> > (2) So I added a command "dev" to our installation script. If you run this after the "mirror" command, it will install all requirements, clone the git repo and build all the CGIs from scratch. This should help you build the CGIs yourself in a fresh VM or Docker container and may also help us track down problems: you can now compare the (pretty simple) yum and make commands in that script with what you use. For example, there is no static linking with any dependencies if you look at the linker command (see below).
> > Here is the version of the script with the "dev" command, it will soon land on github but I am sending you a link right now so you can test it:
> >
> > On a fresh VM or Docker container, you should be able to run these three commands to make a browser mirror and build everything:
> >
> > wget https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh <https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh> <https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh <https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh>>
> > On a fresh VM or Docker container, you should be able to run these three commands to make a browser mirror and build everything:
> >
> > > Can you elaborate what you mean with "accommodate our local mirror" ?
> > >
> > > I just tried an Ubuntu 22 a few days ago and ran the browserSetup.sh script in it and it just worked. I didn't use the docker commands, ran the browserSetup.sh -b install manually but I had a working mirror 2 minutes later.
> > >
> > > I wanted to try Rocky 8 next and unfortunately got distracted by grant reviews...
> > >
> > >
> > >
> > > On Mon, Jan 29, 2024 at 3:38 PM Hoover, David (NIH/CIT) [E] <hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>>> wrote:
> > >
> > > I just tried an Ubuntu 22 a few days ago and ran the browserSetup.sh script in it and it just worked. I didn't use the docker commands, ran the browserSetup.sh -b install manually but I had a working mirror 2 minutes later.
> > >
> > > I wanted to try Rocky 8 next and unfortunately got distracted by grant reviews...
> > >
> > >
> > >
> > >
> > > How up to date is the Docker procedure for the Genome Browser? How difficult would it be to create and use a docker image of the Genome Browser that does not have mysql running internally? We have a substantial mariadb server already full with UCSC data and constantly updated, as well as lots of users' custom tracks. The instructions at https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions>> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions
> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions>>> are very generic and would need to be elaborated to accommodate our local mirror.
> > >
> > > David
> > >
> > > On 1/22/2024 2:44 PM, Christopher Lee wrote:
> > > > Hi Belinda and David,
> > > >
> > > > Unfortunately we are just completely stumped on what is going on here,
> > > > and we do not have the resources to continue looking further. The only
> > > > thing we can say is that we ourselves are upgrading to Rocky 9 soon
> > > > and have verified at least minimal function with that operating
> > > > system, so you can try upgrading and see if that fixes the problem.
> > > >
> > > > As far as theories, we suspect that somehow the MySQL/MariaDb
> > > > installation could be misconfigured, even though that seemed to have
> > > > been ruled out already.
> > > >
> > > > If you do find the cause of the problem and/or a fix, we would of
> > > > course love to hear about it and accept a pull request or fix.
> > > >
> > > > Thanks,
> > > > Christopher Lee
> > > > UCSC Genomics Institute
> > > >
> > > > On Tue, Jan 16, 2024 at 12:07 PM Belinda M. Giardine
> > >
> > > David
> > >
> > > On 1/22/2024 2:44 PM, Christopher Lee wrote:
> > > > Hi Belinda and David,
> > > >
> > > > Unfortunately we are just completely stumped on what is going on here,
> > > > and we do not have the resources to continue looking further. The only
> > > > thing we can say is that we ourselves are upgrading to Rocky 9 soon
> > > > and have verified at least minimal function with that operating
> > > > system, so you can try upgrading and see if that fixes the problem.
> > > >
> > > > As far as theories, we suspect that somehow the MySQL/MariaDb
> > > > installation could be misconfigured, even though that seemed to have
> > > > been ruled out already.
> > > >
> > > > If you do find the cause of the problem and/or a fix, we would of
> > > > course love to hear about it and accept a pull request or fix.
> > > >
> > > > Thanks,
> > > > Christopher Lee
> > > > UCSC Genomics Institute
> > > >
> > > > On Tue, Jan 16, 2024 at 12:07 PM Belinda M. Giardine
> > > > <giar...@bx.psu.edu <mailto:giar...@bx.psu.edu> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>>>> wrote:
> > > >>
> > > >> I put a copy of the files in the cgi-bin here
> > > >> https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/ <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/> <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/ <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/>> <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/ <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/> <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/ <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/>>>
> > > >>
> > > >> I put a copy of the files in the cgi-bin here
> > > >>
> > > >> If you mean you want to be able to access the pages on our server the
> > > >> public version is
> > > >> https://main.genome-browser.bx.psu.edu/ <https://main.genome-browser.bx.psu.edu/> <https://main.genome-browser.bx.psu.edu/ <https://main.genome-browser.bx.psu.edu/>> <https://main.genome-browser.bx.psu.edu/ <https://main.genome-browser.bx.psu.edu/> <https://main.genome-browser.bx.psu.edu/ <https://main.genome-browser.bx.psu.edu/>>>
> > > >> If you mean you want to be able to access the pages on our server the
> > > >> public version is
> > > >>
> > > >> Belinda
> > > >>
> > > >>
> > > >> On Tue, 16 Jan 2024, Jairo Navarro Gonzalez wrote:
> > > >>
> > > >>> Hello,
> > > >>>
> > > >>> Thank you for using the UCSC Genome Browser and reporting your issues.
> > > >>>
> > > >>> Would it be possible to place the binaries in a web-accessible location?
> > > >>> This way, our engineers can have a reproducible case to debug the issue.
> > > >>>
> > > >>> If you have any further questions, please reply to gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu> <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>> <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu> <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>>>.
> > > >> Belinda
> > > >>
> > > >>
> > > >> On Tue, 16 Jan 2024, Jairo Navarro Gonzalez wrote:
> > > >>
> > > >>> Hello,
> > > >>>
> > > >>> Thank you for using the UCSC Genome Browser and reporting your issues.
> > > >>>
> > > >>> Would it be possible to place the binaries in a web-accessible location?
> > > >>> This way, our engineers can have a reproducible case to debug the issue.
> > > >>>
> > > >>> All messages sent to that address are archived on a publicly accessible
> > > >>> Google Groups forum.
> > > >>> If your question includes sensitive data, you may send it instead to
> > > >>> genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu> <mailto:genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>> <mailto:genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu> <mailto:genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>>>.
> > > >>> Google Groups forum.
> > > >>> If your question includes sensitive data, you may send it instead to
> > > >>>
> > > >>> Jairo Navarro
> > > >>> UCSC Genome Browser
> > > >>>
> > > >>> On Tue, Jan 2, 2024 at 8:56?AM Belinda M. Giardine <giar...@bx.psu.edu <mailto:giar...@bx.psu.edu> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>>>>
> > > >>> Jairo Navarro
> > > >>> UCSC Genome Browser
> > > >>>
> > > >>> wrote:
> > > >>>
> > > >>>> We are building our own binaries. It is running on a VM.
> > > >>>>
> > > >>>> Belinda
> > > >>>>
> > > >>>>
> > > >>>> On Fri, 22 Dec 2023, Maximilian Haeussler wrote:
> > > >>>>
> > > >>>>> David and Belinda,
> > > >>>>> thank you for your patience with this, it's hard to debug if we don't
> > > >>>> have
> > > >>>>> access to a machine and can't reproduce the problem. We don't think it's
> > > >>>>> Rocky 9 itself (trying with a VM).
> > > >>>>> Are you both building your own binaries from the source code or are you
> > > >>>>> using our pre-built binaries?
> > > >>>>> thanks
> > > >>>>> Max
> > > >>>>>
> > > >>>>> On Mon, Dec 18, 2023 at 8:31?PM Belinda M. Giardine <giar...@bx.psu.edu <mailto:giar...@bx.psu.edu> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>>>
> > > >>>
> > > >>>> We are building our own binaries. It is running on a VM.
> > > >>>>
> > > >>>> Belinda
> > > >>>>
> > > >>>>
> > > >>>> On Fri, 22 Dec 2023, Maximilian Haeussler wrote:
> > > >>>>
> > > >>>>> David and Belinda,
> > > >>>>> thank you for your patience with this, it's hard to debug if we don't
> > > >>>> have
> > > >>>>> access to a machine and can't reproduce the problem. We don't think it's
> > > >>>>> Rocky 9 itself (trying with a VM).
> > > >>>>> Are you both building your own binaries from the source code or are you
> > > >>>>> using our pre-built binaries?
> > > >>>>> thanks
> > > >>>>> Max
> > > >>>>>
> > > >>>>>
> > > >>>>>>>>>>> wrote:
> > > >>>>>>>>>>>>
> > > >>>>>>>>>>>> Now I am not so sure what is happening.? Here are some
> > > >>>> observations:
> > > >>>>>>>>>>>>
> > > >>>>>>>>>>>> * The timeout issue holds not just for custom tracks, for the
> > > >>>> track
> > > >>>>>>>>>>>> hubs as well
> > > >>>>>>>>>>>> * On the UCSC site, I can load tracks and a hub hosted on our
> > > >>>> local
> > > >>>>>>>>>>>> dataserver (hpc.nih.gov <http://hpc.nih.gov> <http://hpc.nih.gov <http://hpc.nih.gov>> <http://hpc.nih.gov <http://hpc.nih.gov> <http://hpc.nih.gov <http://hpc.nih.gov>>>), and these display normally
> > > >>>>>>>>>>> wrote:
> > > >>>>>>>>>>>>
> > > >>>>>>>>>>>> Now I am not so sure what is happening.? Here are some
> > > >>>> observations:
> > > >>>>>>>>>>>>
> > > >>>>>>>>>>>> * The timeout issue holds not just for custom tracks, for the
> > > >>>> track
> > > >>>>>>>>>>>> hubs as well
> > > >>>>>>>>>>>> * On the UCSC site, I can load tracks and a hub hosted on our
> > > >>>> local
> > > >>>>>>>>>>>>
> > > >>>>>>>>>>>> --
> > > >>>>>>>>>>>>
> > > >>>>>>>>>>>> ---
> > > >>>>>>>>>>>> You received this message because you are subscribed to the Google
> > > >>>>>>>>>>>> Groups "UCSC Genome Browser Mirror-Specific Support" group.
> > > >>>>>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
> > > >>>>>> send
> > > >>>>>>>>>>>> an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu>> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu> <mailto:genome-mirror%252Buns...@soe.ucsc.edu <mailto:genome-mirror%25252Bun...@soe.ucsc.edu>>>.
> > > >>>>>>>>>>>> --
> > > >>>>>>>>>>>>
> > > >>>>>>>>>>>> ---
> > > >>>>>>>>>>>> You received this message because you are subscribed to the Google
> > > >>>>>>>>>>>> Groups "UCSC Genome Browser Mirror-Specific Support" group.
> > > >>>>>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
> > > >>>>>> send
> > > >>>>>>>>>>>> To view this discussion on the web visit
> > > >>>>>>>>>>>>
> > > >>>>>>
> > > >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov>>>
> > > >>>>>>>>>>>>
> > > >>>>>>
> > > >>>>>> .
> > > >>>>>>>>>>>
> > > >>>>>>>>>
> > > >>>>>>>>> --
> > > >>>>>>>>> David Hoover, Ph.D.
> > > >>>>>>>>> Computational Biologist
> > > >>>>>>>>> High Performance Computing Services,
> > > >>>>>>>>> Center for Information Technology,
> > > >>>>>>>>> National Institutes of Health
> > > >>>>>>>>> 12 South Dr., Rm 2N207
> > > >>>>>>>>> Bethesda, MD 20892, USA
> > > >>>>>>>>> TEL: (+1) 301-435-2986
> > > >>>>>>>>> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>>
> > > >>>>>>>>>>>
> > > >>>>>>>>>
> > > >>>>>>>>> --
> > > >>>>>>>>> David Hoover, Ph.D.
> > > >>>>>>>>> Computational Biologist
> > > >>>>>>>>> High Performance Computing Services,
> > > >>>>>>>>> Center for Information Technology,
> > > >>>>>>>>> National Institutes of Health
> > > >>>>>>>>> 12 South Dr., Rm 2N207
> > > >>>>>>>>> Bethesda, MD 20892, USA
> > > >>>>>>>>> TEL: (+1) 301-435-2986
> > > >>>>>>>>>
> > > >>>>>>>>> --
> > > >>>>>>>>>
> > > >>>>>>>>> ---
> > > >>>>>>>>> You received this message because you are subscribed to the Google
> > > >>>>>> Groups
> > > >>>>>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > > >>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
> > > >>>> send
> > > >>>>>> an
> > > >>>>>>>>> email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu>> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu> <mailto:genome-mirror%252Buns...@soe.ucsc.edu <mailto:genome-mirror%25252Bun...@soe.ucsc.edu>>>.
> > > >>>>>>>>> --
> > > >>>>>>>>>
> > > >>>>>>>>> ---
> > > >>>>>>>>> You received this message because you are subscribed to the Google
> > > >>>>>> Groups
> > > >>>>>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > > >>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
> > > >>>> send
> > > >>>>>> an
> > > >>>>>>>>> To view this discussion on the web visit
> > > >>>>>>>>>
> > > >>>>>>
> > > >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov>>>
> > > >>>>>>>>>
> > > >>>>>>
> > > >>>>>> .
> > > >>>>>>>
> > > >>>>>>> --
> > > >>>>>>> David Hoover, Ph.D.
> > > >>>>>>> Computational Biologist
> > > >>>>>>> High Performance Computing Services,
> > > >>>>>>> Center for Information Technology,
> > > >>>>>>> National Institutes of Health
> > > >>>>>>> 12 South Dr., Rm 2N207
> > > >>>>>>> Bethesda, MD 20892, USA
> > > >>>>>>> TEL: (+1) 301-435-2986
> > > >>>>>>> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>>
> > > >>>>>>>
> > > >>>>>>> --
> > > >>>>>>> David Hoover, Ph.D.
> > > >>>>>>> Computational Biologist
> > > >>>>>>> High Performance Computing Services,
> > > >>>>>>> Center for Information Technology,
> > > >>>>>>> National Institutes of Health
> > > >>>>>>> 12 South Dr., Rm 2N207
> > > >>>>>>> Bethesda, MD 20892, USA
> > > >>>>>>> TEL: (+1) 301-435-2986
> > > >>>>>>>
> > > >>>>>>> --
> > > >>>>>>>
> > > >>>>>>> --- You received this message because you are subscribed to the Google
> > > >>>>>> Groups
> > > >>>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > > >>>>>>> To unsubscribe from this group and stop receiving emails from it, send
> > > >>>>>> an
> > > >>>>>>> email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu>> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu> <mailto:genome-mirror%252Buns...@soe.ucsc.edu <mailto:genome-mirror%25252Bun...@soe.ucsc.edu>>>.
> > > >>>>>>> --
> > > >>>>>>>
> > > >>>>>>> --- You received this message because you are subscribed to the Google
> > > >>>>>> Groups
> > > >>>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > > >>>>>>> To unsubscribe from this group and stop receiving emails from it, send
> > > >>>>>> an
> > > >>>>>>> To view this discussion on the web visit
> > > >>>>>>>
> > > >>>>>>
> > > >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov>>>
> > > >>>>>>>
> > > >>>>>>
> > > >>>>>> .
> > > >>>>>>>
> > > >>>>>>>
> > > >>>>>>
> > > >>>>>> --
> > > >>>>>>
> > > >>>>>> ---
> > > >>>>>> You received this message because you are subscribed to the Google
> > > >>>> Groups
> > > >>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > > >>>>>> To unsubscribe from this group and stop receiving emails from it, send
> > > >>>> an
> > > >>>>>> email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu>> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu> <mailto:genome-mirror%252Buns...@soe.ucsc.edu <mailto:genome-mirror%25252Bun...@soe.ucsc.edu>>>.
> > > >>>>>>>
> > > >>>>>>>
> > > >>>>>>
> > > >>>>>> --
> > > >>>>>>
> > > >>>>>> ---
> > > >>>>>> You received this message because you are subscribed to the Google
> > > >>>> Groups
> > > >>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > > >>>>>> To unsubscribe from this group and stop receiving emails from it, send
> > > >>>> an
> > > >>>>>> To view this discussion on the web visit
> > > >>>>>>
> > > >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu
> > > >>>>>>
> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu>>>
> > > >>>>>> .
> > > >>>>>>
> > > >>>>>
> > > >>>>
> > > >>>> --
> > > >>>>
> > > >>>> ---
> > > >>>> You received this message because you are subscribed to the Google Groups
> > > >>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > > >>>> To unsubscribe from this group and stop receiving emails from it, send an
> > > >>>> email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu>> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu> <mailto:genome-mirror%252Buns...@soe.ucsc.edu <mailto:genome-mirror%25252Bun...@soe.ucsc.edu>>>.
> > > >>>>>> .
> > > >>>>>>
> > > >>>>>
> > > >>>>
> > > >>>> --
> > > >>>>
> > > >>>> ---
> > > >>>> You received this message because you are subscribed to the Google Groups
> > > >>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > > >>>> To unsubscribe from this group and stop receiving emails from it, send an
> > > >>>> To view this discussion on the web visit
> > > >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu>>>
> > > >>>> .
> > > >>>>
> > > >>>
> > >
> > > --
> > > David Hoover, Ph.D.
> > > Computational Biologist
> > > High Performance Computing Services,
> > > Center for Information Technology,
> > > National Institutes of Health
> > > 12 South Dr., Rm 2N207
> > > Bethesda, MD 20892, USA
> > > TEL: (+1) 301-435-2986
> > > Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>>
> > > >>>>
> > > >>>
> > >
> > > --
> > > David Hoover, Ph.D.
> > > Computational Biologist
> > > High Performance Computing Services,
> > > Center for Information Technology,
> > > National Institutes of Health
> > > 12 South Dr., Rm 2N207
> > > Bethesda, MD 20892, USA
> > > TEL: (+1) 301-435-2986
> > >
> > > --
> > >
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> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com?utm_medium=email&utm_source=footer <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com?utm_medium=email&utm_source=footer>>>.
> >
> > --
> > David Hoover, Ph.D.
> > Computational Biologist
> > High Performance Computing Services,
> > Center for Information Technology,
> > National Institutes of Health
> > 12 South Dr., Rm 2N207
> > Bethesda, MD 20892, USA
> > TEL: (+1) 301-435-2986
> >
> > --
> > David Hoover, Ph.D.
> > Computational Biologist
> > High Performance Computing Services,
> > Center for Information Technology,
> > National Institutes of Health
> > 12 South Dr., Rm 2N207
> > Bethesda, MD 20892, USA
> > TEL: (+1) 301-435-2986
> > Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>
> >
> > --
> >
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> > To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu>>.
> > To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fy8z%2B%3DmSyDipxamf4P5CFP1YTO_kFyrBW5B-CO%3DHxSQ4A%40mail.gmail.com <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fy8z%2B%3DmSyDipxamf4P5CFP1YTO_kFyrBW5B-CO%3DHxSQ4A%40mail.gmail.com> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fy8z%2B%3DmSyDipxamf4P5CFP1YTO_kFyrBW5B-CO%3DHxSQ4A%40mail.gmail.com?utm_medium=email&utm_source=footer <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fy8z%2B%3DmSyDipxamf4P5CFP1YTO_kFyrBW5B-CO%3DHxSQ4A%40mail.gmail.com?utm_medium=email&utm_source=footer>>.
> >
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>
> --
> David Hoover, Ph.D.
> Computational Biologist
> High Performance Computing Services,
> Center for Information Technology,
> National Institutes of Health
> 12 South Dr., Rm 2N207
> Bethesda, MD 20892, USA
> TEL: (+1) 301-435-2986
> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>
> --
> David Hoover, Ph.D.
> Computational Biologist
> High Performance Computing Services,
> Center for Information Technology,
> National Institutes of Health
> 12 South Dr., Rm 2N207
> Bethesda, MD 20892, USA
> TEL: (+1) 301-435-2986
>
> --
>
> ---
> You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu>.
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>
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>
> ---
> You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
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Hoover, David (NIH/CIT) [E]
Feb 13, 2024, 9:22:55 AM2/13/24
to Maximilian Haeussler, genome...@soe.ucsc.edu
No luck. Removing the final '/' from login.browserAddr did not solve the problem. I changed the values of wiki.userNameCookie and wiki.loggedInCookie to the defaults and that didn't help either.
When I click the 'Login' button, the page flashes up the following message for a few seconds, but then reverts to the hgSession page without actually logging me in:
Login successful for user *****
Helix Systems Genome Browser
Login successful, setting cookies now...
The second line is the value of login.BrowserName.
I tried creating a new account, but the email never went through. Is there something that needs to be set in the Docker container to allow mail to get sent?
David
On 2/13/2024 8:23 AM, Maximilian Haeussler wrote:
> Hi David,
>
> great!
>
> this has to do with the cookies... but I don't think I've ever had this problem before. Hmm. Can you try removing the trailing "/" from the browserAddr?
> login.mailSignature=Helix Systems Staff
> login.mailReturnAddr=webt...@helix.nih.gov <mailto:webt...@helix.nih.gov>
> > > > https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions>> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions>>> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions
> > > > >>>>>> genome.ucsc.edu <http://genome.ucsc.edu> <http://genome.ucsc.edu <http://genome.ucsc.edu>> <http://genome.ucsc.edu <http://genome.ucsc.edu> <http://genome.ucsc.edu <http://genome.ucsc.edu>>> <http://genome.ucsc.edu <http://genome.ucsc.edu> <http://genome.ucsc.edu <http://genome.ucsc.edu>> <http://genome.ucsc.edu <http://genome.ucsc.edu> <http://genome.ucsc.edu <http://genome.ucsc.edu>>>>
> > > > >>>>>>>>>>> Genome Browser Mirror-Specific Support <genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu> <mailto:genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu>> <mailto:genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu> <mailto:genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu>>> <mailto:genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu> <mailto:genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu>> <mailto:genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu> <mailto:genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu>>>>
> > > > >>>>>>>>>>>> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>>>
> > > > To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com>
> > To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/4873e9c1-f343-801b-5067-ee805a140150%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/4873e9c1-f343-801b-5067-ee805a140150%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/4873e9c1-f343-801b-5067-ee805a140150%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/4873e9c1-f343-801b-5067-ee805a140150%40hpc.nih.gov>>.
When I click the 'Login' button, the page flashes up the following message for a few seconds, but then reverts to the hgSession page without actually logging me in:
Login successful for user *****
Helix Systems Genome Browser
Login successful, setting cookies now...
The second line is the value of login.BrowserName.
I tried creating a new account, but the email never went through. Is there something that needs to be set in the Docker container to allow mail to get sent?
David
On 2/13/2024 8:23 AM, Maximilian Haeussler wrote:
> Hi David,
>
> great!
>
> this has to do with the cookies... but I don't think I've ever had this problem before. Hmm. Can you try removing the trailing "/" from the browserAddr?
>
>
> On Mon, Feb 12, 2024 at 7:32 PM 'Hoover, David (NIH/CIT) [E]' via UCSC Genome Browser Mirror-Specific Support <genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu>> wrote:
>
> Max,
>
> I've gotten the docker version of the Genome Browser up and running. I managed to edit hg.conf so that it uses our local mariadb server. I can create custom tracks and everything works well.
>
> However, one thing that is still broken. When I attempt to log into my local GB account using the hgLogin executable, it authenticates but then immediately signs me out. Do you have any idea what might be going wrong?
>
> Here are my changes to hg.conf:
>
> wiki.userNameCookie=wikidb_mw1_UserName
> wiki.loggedInCookie=wikidb_mw1_UserID
> wiki.host=HTTPHOST
> login.systemName=UCSC Genome Browser Mirror
> login.browserName=Helix Systems Genome Browser
> login.browserAddr=10.1.201.160:8080/ <http://10.1.201.160:8080/>
>
> On Mon, Feb 12, 2024 at 7:32 PM 'Hoover, David (NIH/CIT) [E]' via UCSC Genome Browser Mirror-Specific Support <genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu>> wrote:
>
> Max,
>
> I've gotten the docker version of the Genome Browser up and running. I managed to edit hg.conf so that it uses our local mariadb server. I can create custom tracks and everything works well.
>
> However, one thing that is still broken. When I attempt to log into my local GB account using the hgLogin executable, it authenticates but then immediately signs me out. Do you have any idea what might be going wrong?
>
> Here are my changes to hg.conf:
>
> wiki.userNameCookie=wikidb_mw1_UserName
> wiki.loggedInCookie=wikidb_mw1_UserID
> wiki.host=HTTPHOST
> login.systemName=UCSC Genome Browser Mirror
> login.browserName=Helix Systems Genome Browser
> login.mailSignature=Helix Systems Staff
> login.mailReturnAddr=webt...@helix.nih.gov <mailto:webt...@helix.nih.gov>
>
> David
>
> On 2/9/2024 12:56 PM, 'Maximilian Haeussler' via UCSC Genome Browser Mirror-Specific Support wrote:
> > The script should have switched off selinux, did that not work?
> >
> > On Fri, Feb 9, 2024 at 6:46 PM 'Hoover, David (NIH/CIT) [E]' via UCSC Genome Browser Mirror-Specific Support <genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu> <mailto:genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu>>> wrote:
> >
> > When you run the Genome Browser under rocky8, do you have selinux enabled?
> >
> > David
> >
> > On 2/5/2024 11:22 AM, 'Maximilian Haeussler' via UCSC Genome Browser Mirror-Specific Support wrote:
> > > Hi David,
> > >
> > > OK, I've spent time on this, but still can't reproduce it:
> > >
> > > (1) Took an empty Rocky 8 VM on my laptop, installed and built the CGIs there, but can access hubs just fine. I'm not getting the error that you saw. I tried the Alfa hub, as this is also on the NIH campus:
> > > https://ftp.ncbi.nlm.nih.gov/snp/population_frequency/TrackHub/latest/hub.txt <https://ftp.ncbi.nlm.nih.gov/snp/population_frequency/TrackHub/latest/hub.txt> <https://ftp.ncbi.nlm.nih.gov/snp/population_frequency/TrackHub/latest/hub.txt <https://ftp.ncbi.nlm.nih.gov/snp/population_frequency/TrackHub/latest/hub.txt>> <https://ftp.ncbi.nlm.nih.gov/snp/population_frequency/TrackHub/latest/hub.txt <https://ftp.ncbi.nlm.nih.gov/snp/population_frequency/TrackHub/latest/hub.txt> <https://ftp.ncbi.nlm.nih.gov/snp/population_frequency/TrackHub/latest/hub.txt <https://ftp.ncbi.nlm.nih.gov/snp/population_frequency/TrackHub/latest/hub.txt>>>. It displays without errors...
> David
>
> On 2/9/2024 12:56 PM, 'Maximilian Haeussler' via UCSC Genome Browser Mirror-Specific Support wrote:
> > The script should have switched off selinux, did that not work?
> >
> > On Fri, Feb 9, 2024 at 6:46 PM 'Hoover, David (NIH/CIT) [E]' via UCSC Genome Browser Mirror-Specific Support <genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu> <mailto:genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu>>> wrote:
> >
> > When you run the Genome Browser under rocky8, do you have selinux enabled?
> >
> > David
> >
> > On 2/5/2024 11:22 AM, 'Maximilian Haeussler' via UCSC Genome Browser Mirror-Specific Support wrote:
> > > Hi David,
> > >
> > > OK, I've spent time on this, but still can't reproduce it:
> > >
> > > (1) Took an empty Rocky 8 VM on my laptop, installed and built the CGIs there, but can access hubs just fine. I'm not getting the error that you saw. I tried the Alfa hub, as this is also on the NIH campus:
> > >
> > > (2) So I added a command "dev" to our installation script. If you run this after the "mirror" command, it will install all requirements, clone the git repo and build all the CGIs from scratch. This should help you build the CGIs yourself in a fresh VM or Docker container and may also help us track down problems: you can now compare the (pretty simple) yum and make commands in that script with what you use. For example, there is no static linking with any dependencies if you look at the linker command (see below).
> > > Here is the version of the script with the "dev" command, it will soon land on github but I am sending you a link right now so you can test it:
> > > https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh <https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh> <https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh <https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh>> <https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh <https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh> <https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh <https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh>>>
> > > (2) So I added a command "dev" to our installation script. If you run this after the "mirror" command, it will install all requirements, clone the git repo and build all the CGIs from scratch. This should help you build the CGIs yourself in a fresh VM or Docker container and may also help us track down problems: you can now compare the (pretty simple) yum and make commands in that script with what you use. For example, there is no static linking with any dependencies if you look at the linker command (see below).
> > > Here is the version of the script with the "dev" command, it will soon land on github but I am sending you a link right now so you can test it:
> > >
> > > On a fresh VM or Docker container, you should be able to run these three commands to make a browser mirror and build everything:
> > >
> > > wget https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh <https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh> <https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh <https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh>> <https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh <https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh> <https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh <https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh>>>
> > > On a fresh VM or Docker container, you should be able to run these three commands to make a browser mirror and build everything:
> > >
> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions>> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions>>>>
> > > > Can you elaborate what you mean with "accommodate our local mirror" ?
> > > >
> > > > I just tried an Ubuntu 22 a few days ago and ran the browserSetup.sh script in it and it just worked. I didn't use the docker commands, ran the browserSetup.sh -b install manually but I had a working mirror 2 minutes later.
> > > >
> > > > I wanted to try Rocky 8 next and unfortunately got distracted by grant reviews...
> > > >
> > > >
> > > >
> > > > On Mon, Jan 29, 2024 at 3:38 PM Hoover, David (NIH/CIT) [E] <hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>>>> wrote:
> > > >
> > > > How up to date is the Docker procedure for the Genome Browser? How difficult would it be to create and use a docker image of the Genome Browser that does not have mysql running internally? We have a substantial mariadb server already full with UCSC data and constantly updated, as well as lots of users' custom tracks. The instructions at https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions>> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions
> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions>>> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions>> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions>
> > > > Can you elaborate what you mean with "accommodate our local mirror" ?
> > > >
> > > > I just tried an Ubuntu 22 a few days ago and ran the browserSetup.sh script in it and it just worked. I didn't use the docker commands, ran the browserSetup.sh -b install manually but I had a working mirror 2 minutes later.
> > > >
> > > > I wanted to try Rocky 8 next and unfortunately got distracted by grant reviews...
> > > >
> > > >
> > > >
> > > > On Mon, Jan 29, 2024 at 3:38 PM Hoover, David (NIH/CIT) [E] <hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>>>> wrote:
> > > >
> > > > How up to date is the Docker procedure for the Genome Browser? How difficult would it be to create and use a docker image of the Genome Browser that does not have mysql running internally? We have a substantial mariadb server already full with UCSC data and constantly updated, as well as lots of users' custom tracks. The instructions at https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions>> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions
> > <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions>>>> are very generic and would need to be elaborated to accommodate our local mirror.
> > > >
> > > > David
> > > >
> > > > On 1/22/2024 2:44 PM, Christopher Lee wrote:
> > > > > Hi Belinda and David,
> > > > >
> > > > > Unfortunately we are just completely stumped on what is going on here,
> > > > > and we do not have the resources to continue looking further. The only
> > > > > thing we can say is that we ourselves are upgrading to Rocky 9 soon
> > > > > and have verified at least minimal function with that operating
> > > > > system, so you can try upgrading and see if that fixes the problem.
> > > > >
> > > > > As far as theories, we suspect that somehow the MySQL/MariaDb
> > > > > installation could be misconfigured, even though that seemed to have
> > > > > been ruled out already.
> > > > >
> > > > > If you do find the cause of the problem and/or a fix, we would of
> > > > > course love to hear about it and accept a pull request or fix.
> > > > >
> > > > > Thanks,
> > > > > Christopher Lee
> > > > > UCSC Genomics Institute
> > > > >
> > > > > On Tue, Jan 16, 2024 at 12:07 PM Belinda M. Giardine
> > > >
> > > > David
> > > >
> > > > On 1/22/2024 2:44 PM, Christopher Lee wrote:
> > > > > Hi Belinda and David,
> > > > >
> > > > > Unfortunately we are just completely stumped on what is going on here,
> > > > > and we do not have the resources to continue looking further. The only
> > > > > thing we can say is that we ourselves are upgrading to Rocky 9 soon
> > > > > and have verified at least minimal function with that operating
> > > > > system, so you can try upgrading and see if that fixes the problem.
> > > > >
> > > > > As far as theories, we suspect that somehow the MySQL/MariaDb
> > > > > installation could be misconfigured, even though that seemed to have
> > > > > been ruled out already.
> > > > >
> > > > > If you do find the cause of the problem and/or a fix, we would of
> > > > > course love to hear about it and accept a pull request or fix.
> > > > >
> > > > > Thanks,
> > > > > Christopher Lee
> > > > > UCSC Genomics Institute
> > > > >
> > > > > On Tue, Jan 16, 2024 at 12:07 PM Belinda M. Giardine
> > > > > <giar...@bx.psu.edu <mailto:giar...@bx.psu.edu> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>>> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>>>>> wrote:
> > > > >>
> > > > >> I put a copy of the files in the cgi-bin here
> > > > >> https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/ <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/> <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/ <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/>> <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/ <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/> <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/ <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/>>> <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/ <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/> <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/ <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/>> <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/ <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/> <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/ <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/>>>>
> > > > >>
> > > > >> I put a copy of the files in the cgi-bin here
> > > > >>
> > > > >> If you mean you want to be able to access the pages on our server the
> > > > >> public version is
> > > > >> https://main.genome-browser.bx.psu.edu/ <https://main.genome-browser.bx.psu.edu/> <https://main.genome-browser.bx.psu.edu/ <https://main.genome-browser.bx.psu.edu/>> <https://main.genome-browser.bx.psu.edu/ <https://main.genome-browser.bx.psu.edu/> <https://main.genome-browser.bx.psu.edu/ <https://main.genome-browser.bx.psu.edu/>>> <https://main.genome-browser.bx.psu.edu/ <https://main.genome-browser.bx.psu.edu/> <https://main.genome-browser.bx.psu.edu/ <https://main.genome-browser.bx.psu.edu/>> <https://main.genome-browser.bx.psu.edu/ <https://main.genome-browser.bx.psu.edu/> <https://main.genome-browser.bx.psu.edu/ <https://main.genome-browser.bx.psu.edu/>>>>
> > > > >> If you mean you want to be able to access the pages on our server the
> > > > >> public version is
> > > > >>
> > > > >> Belinda
> > > > >>
> > > > >>
> > > > >> On Tue, 16 Jan 2024, Jairo Navarro Gonzalez wrote:
> > > > >>
> > > > >>> Hello,
> > > > >>>
> > > > >>> Thank you for using the UCSC Genome Browser and reporting your issues.
> > > > >>>
> > > > >>> Would it be possible to place the binaries in a web-accessible location?
> > > > >>> This way, our engineers can have a reproducible case to debug the issue.
> > > > >>>
> > > > >>> If you have any further questions, please reply to gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu> <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>> <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu> <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>>> <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu> <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>> <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu> <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>>>>.
> > > > >> Belinda
> > > > >>
> > > > >>
> > > > >> On Tue, 16 Jan 2024, Jairo Navarro Gonzalez wrote:
> > > > >>
> > > > >>> Hello,
> > > > >>>
> > > > >>> Thank you for using the UCSC Genome Browser and reporting your issues.
> > > > >>>
> > > > >>> Would it be possible to place the binaries in a web-accessible location?
> > > > >>> This way, our engineers can have a reproducible case to debug the issue.
> > > > >>>
> > > > >>> All messages sent to that address are archived on a publicly accessible
> > > > >>> Google Groups forum.
> > > > >>> If your question includes sensitive data, you may send it instead to
> > > > >>> genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu> <mailto:genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>> <mailto:genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu> <mailto:genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>>> <mailto:genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu> <mailto:genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>> <mailto:genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu> <mailto:genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>>>>.
> > > > >>> Google Groups forum.
> > > > >>> If your question includes sensitive data, you may send it instead to
> > > > >>>
> > > > >>> Jairo Navarro
> > > > >>> UCSC Genome Browser
> > > > >>>
> > > > >>> On Tue, Jan 2, 2024 at 8:56?AM Belinda M. Giardine <giar...@bx.psu.edu <mailto:giar...@bx.psu.edu> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>>> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>>>>>
> > > > >>> Jairo Navarro
> > > > >>> UCSC Genome Browser
> > > > >>>
> > > > >>> wrote:
> > > > >>>
> > > > >>>> We are building our own binaries. It is running on a VM.
> > > > >>>>
> > > > >>>> Belinda
> > > > >>>>
> > > > >>>>
> > > > >>>> On Fri, 22 Dec 2023, Maximilian Haeussler wrote:
> > > > >>>>
> > > > >>>>> David and Belinda,
> > > > >>>>> thank you for your patience with this, it's hard to debug if we don't
> > > > >>>> have
> > > > >>>>> access to a machine and can't reproduce the problem. We don't think it's
> > > > >>>>> Rocky 9 itself (trying with a VM).
> > > > >>>>> Are you both building your own binaries from the source code or are you
> > > > >>>>> using our pre-built binaries?
> > > > >>>>> thanks
> > > > >>>>> Max
> > > > >>>>>
> > > > >>>>> On Mon, Dec 18, 2023 at 8:31?PM Belinda M. Giardine <giar...@bx.psu.edu <mailto:giar...@bx.psu.edu> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>>> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>>>>
> > > > >>>
> > > > >>>> We are building our own binaries. It is running on a VM.
> > > > >>>>
> > > > >>>> Belinda
> > > > >>>>
> > > > >>>>
> > > > >>>> On Fri, 22 Dec 2023, Maximilian Haeussler wrote:
> > > > >>>>
> > > > >>>>> David and Belinda,
> > > > >>>>> thank you for your patience with this, it's hard to debug if we don't
> > > > >>>> have
> > > > >>>>> access to a machine and can't reproduce the problem. We don't think it's
> > > > >>>>> Rocky 9 itself (trying with a VM).
> > > > >>>>> Are you both building your own binaries from the source code or are you
> > > > >>>>> using our pre-built binaries?
> > > > >>>>> thanks
> > > > >>>>> Max
> > > > >>>>>
> > > > >>>>>
> > > > >>>>>>>>>>> wrote:
> > > > >>>>>>>>>>>>
> > > > >>>>>>>>>>>> Now I am not so sure what is happening.? Here are some
> > > > >>>> observations:
> > > > >>>>>>>>>>>>
> > > > >>>>>>>>>>>> * The timeout issue holds not just for custom tracks, for the
> > > > >>>> track
> > > > >>>>>>>>>>>> hubs as well
> > > > >>>>>>>>>>>> * On the UCSC site, I can load tracks and a hub hosted on our
> > > > >>>> local
> > > > >>>>>>>>>>>> dataserver (hpc.nih.gov <http://hpc.nih.gov> <http://hpc.nih.gov <http://hpc.nih.gov>> <http://hpc.nih.gov <http://hpc.nih.gov> <http://hpc.nih.gov <http://hpc.nih.gov>>> <http://hpc.nih.gov <http://hpc.nih.gov> <http://hpc.nih.gov <http://hpc.nih.gov>> <http://hpc.nih.gov <http://hpc.nih.gov> <http://hpc.nih.gov <http://hpc.nih.gov>>>>), and these display normally
> > > > >>>>>>>>>>> wrote:
> > > > >>>>>>>>>>>>
> > > > >>>>>>>>>>>> Now I am not so sure what is happening.? Here are some
> > > > >>>> observations:
> > > > >>>>>>>>>>>>
> > > > >>>>>>>>>>>> * The timeout issue holds not just for custom tracks, for the
> > > > >>>> track
> > > > >>>>>>>>>>>> hubs as well
> > > > >>>>>>>>>>>> * On the UCSC site, I can load tracks and a hub hosted on our
> > > > >>>> local
> > > > >>>>>>>>>>>>
> > > > >>>>>>>>>>>> --
> > > > >>>>>>>>>>>>
> > > > >>>>>>>>>>>> ---
> > > > >>>>>>>>>>>> You received this message because you are subscribed to the Google
> > > > >>>>>>>>>>>> Groups "UCSC Genome Browser Mirror-Specific Support" group.
> > > > >>>>>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
> > > > >>>>>> send
> > > > >>>>>>>>>>>> an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu>> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu> <mailto:genome-mirror%252Buns...@soe.ucsc.edu <mailto:genome-mirror%25252Bun...@soe.ucsc.edu>>> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu> <mailto:genome-mirror%252Buns...@soe.ucsc.edu <mailto:genome-mirror%25252Bun...@soe.ucsc.edu>> <mailto:genome-mirror%252Buns...@soe.ucsc.edu <mailto:genome-mirror%25252Bun...@soe.ucsc.edu> <mailto:genome-mirror%25252Bun...@soe.ucsc.edu <mailto:genome-mirror%2525252Bu...@soe.ucsc.edu>>>>.
> > > > >>>>>>>>>>>> --
> > > > >>>>>>>>>>>>
> > > > >>>>>>>>>>>> ---
> > > > >>>>>>>>>>>> You received this message because you are subscribed to the Google
> > > > >>>>>>>>>>>> Groups "UCSC Genome Browser Mirror-Specific Support" group.
> > > > >>>>>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
> > > > >>>>>> send
> > > > >>>>>>>>>>>> To view this discussion on the web visit
> > > > >>>>>>>>>>>>
> > > > >>>>>>
> > > > >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov>>>
> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov>>>>
> > > > >>>>>> .
> > > > >>>>>>>>>>>
> > > > >>>>>>>>>
> > > > >>>>>>>>> --
> > > > >>>>>>>>> David Hoover, Ph.D.
> > > > >>>>>>>>> Computational Biologist
> > > > >>>>>>>>> High Performance Computing Services,
> > > > >>>>>>>>> Center for Information Technology,
> > > > >>>>>>>>> National Institutes of Health
> > > > >>>>>>>>> 12 South Dr., Rm 2N207
> > > > >>>>>>>>> Bethesda, MD 20892, USA
> > > > >>>>>>>>> TEL: (+1) 301-435-2986
> > > > >>>>>>>>> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>>>
> > > > >>>>>>>>>>>>
> > > > >>>>>>
> > > > >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov>>>
> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov>>>>
> > > > >>>>>> .
> > > > >>>>>>>>>>>
> > > > >>>>>>>>>
> > > > >>>>>>>>> --
> > > > >>>>>>>>> David Hoover, Ph.D.
> > > > >>>>>>>>> Computational Biologist
> > > > >>>>>>>>> High Performance Computing Services,
> > > > >>>>>>>>> Center for Information Technology,
> > > > >>>>>>>>> National Institutes of Health
> > > > >>>>>>>>> 12 South Dr., Rm 2N207
> > > > >>>>>>>>> Bethesda, MD 20892, USA
> > > > >>>>>>>>> TEL: (+1) 301-435-2986
> > > > >>>>>>>>>
> > > > >>>>>>>>> --
> > > > >>>>>>>>>
> > > > >>>>>>>>> ---
> > > > >>>>>>>>> You received this message because you are subscribed to the Google
> > > > >>>>>> Groups
> > > > >>>>>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > > > >>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
> > > > >>>> send
> > > > >>>>>> an
> > > > >>>>>>>>> email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu>> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu> <mailto:genome-mirror%252Buns...@soe.ucsc.edu <mailto:genome-mirror%25252Bun...@soe.ucsc.edu>>> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu> <mailto:genome-mirror%252Buns...@soe.ucsc.edu <mailto:genome-mirror%25252Bun...@soe.ucsc.edu>> <mailto:genome-mirror%252Buns...@soe.ucsc.edu <mailto:genome-mirror%25252Bun...@soe.ucsc.edu> <mailto:genome-mirror%25252Bun...@soe.ucsc.edu <mailto:genome-mirror%2525252Bu...@soe.ucsc.edu>>>>.
> > > > >>>>>>>>> --
> > > > >>>>>>>>>
> > > > >>>>>>>>> ---
> > > > >>>>>>>>> You received this message because you are subscribed to the Google
> > > > >>>>>> Groups
> > > > >>>>>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > > > >>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
> > > > >>>> send
> > > > >>>>>> an
> > > > >>>>>>>>> To view this discussion on the web visit
> > > > >>>>>>>>>
> > > > >>>>>>
> > > > >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov>>>
> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov>>>>
> > > > >>>>>> .
> > > > >>>>>>>
> > > > >>>>>>> --
> > > > >>>>>>> David Hoover, Ph.D.
> > > > >>>>>>> Computational Biologist
> > > > >>>>>>> High Performance Computing Services,
> > > > >>>>>>> Center for Information Technology,
> > > > >>>>>>> National Institutes of Health
> > > > >>>>>>> 12 South Dr., Rm 2N207
> > > > >>>>>>> Bethesda, MD 20892, USA
> > > > >>>>>>> TEL: (+1) 301-435-2986
> > > > >>>>>>> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>>>
> > > > >>>>>>>>>
> > > > >>>>>>
> > > > >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov>>>
> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov>>>>
> > > > >>>>>> .
> > > > >>>>>>>
> > > > >>>>>>> --
> > > > >>>>>>> David Hoover, Ph.D.
> > > > >>>>>>> Computational Biologist
> > > > >>>>>>> High Performance Computing Services,
> > > > >>>>>>> Center for Information Technology,
> > > > >>>>>>> National Institutes of Health
> > > > >>>>>>> 12 South Dr., Rm 2N207
> > > > >>>>>>> Bethesda, MD 20892, USA
> > > > >>>>>>> TEL: (+1) 301-435-2986
> > > > >>>>>>>
> > > > >>>>>>> --
> > > > >>>>>>>
> > > > >>>>>>> --- You received this message because you are subscribed to the Google
> > > > >>>>>> Groups
> > > > >>>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > > > >>>>>>> To unsubscribe from this group and stop receiving emails from it, send
> > > > >>>>>> an
> > > > >>>>>>> email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu>> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu> <mailto:genome-mirror%252Buns...@soe.ucsc.edu <mailto:genome-mirror%25252Bun...@soe.ucsc.edu>>> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu> <mailto:genome-mirror%252Buns...@soe.ucsc.edu <mailto:genome-mirror%25252Bun...@soe.ucsc.edu>> <mailto:genome-mirror%252Buns...@soe.ucsc.edu <mailto:genome-mirror%25252Bun...@soe.ucsc.edu> <mailto:genome-mirror%25252Bun...@soe.ucsc.edu <mailto:genome-mirror%2525252Bu...@soe.ucsc.edu>>>>.
> > > > >>>>>>> --
> > > > >>>>>>>
> > > > >>>>>>> --- You received this message because you are subscribed to the Google
> > > > >>>>>> Groups
> > > > >>>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > > > >>>>>>> To unsubscribe from this group and stop receiving emails from it, send
> > > > >>>>>> an
> > > > >>>>>>> To view this discussion on the web visit
> > > > >>>>>>>
> > > > >>>>>>
> > > > >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov>>>
> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov>>>>
> > > > >>>>>> .
> > > > >>>>>>>
> > > > >>>>>>>
> > > > >>>>>>
> > > > >>>>>> --
> > > > >>>>>>
> > > > >>>>>> ---
> > > > >>>>>> You received this message because you are subscribed to the Google
> > > > >>>> Groups
> > > > >>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > > > >>>>>> To unsubscribe from this group and stop receiving emails from it, send
> > > > >>>> an
> > > > >>>>>> email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu>> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu> <mailto:genome-mirror%252Buns...@soe.ucsc.edu <mailto:genome-mirror%25252Bun...@soe.ucsc.edu>>> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu> <mailto:genome-mirror%252Buns...@soe.ucsc.edu <mailto:genome-mirror%25252Bun...@soe.ucsc.edu>> <mailto:genome-mirror%252Buns...@soe.ucsc.edu <mailto:genome-mirror%25252Bun...@soe.ucsc.edu> <mailto:genome-mirror%25252Bun...@soe.ucsc.edu <mailto:genome-mirror%2525252Bu...@soe.ucsc.edu>>>>.
> > > > >>>>>>>
> > > > >>>>>>
> > > > >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov>>>
> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov>>>>
> > > > >>>>>> .
> > > > >>>>>>>
> > > > >>>>>>>
> > > > >>>>>>
> > > > >>>>>> --
> > > > >>>>>>
> > > > >>>>>> ---
> > > > >>>>>> You received this message because you are subscribed to the Google
> > > > >>>> Groups
> > > > >>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > > > >>>>>> To unsubscribe from this group and stop receiving emails from it, send
> > > > >>>> an
> > > > >>>>>> To view this discussion on the web visit
> > > > >>>>>>
> > > > >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu
> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu>>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu>
> > > > >>>>>>
> > > > >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu
> > <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu>>>>
> > > > >>>>>> .
> > > > >>>>>>
> > > > >>>>>
> > > > >>>>
> > > > >>>> --
> > > > >>>>
> > > > >>>> ---
> > > > >>>> You received this message because you are subscribed to the Google Groups
> > > > >>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > > > >>>> To unsubscribe from this group and stop receiving emails from it, send an
> > > > >>>> email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu>> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu> <mailto:genome-mirror%252Buns...@soe.ucsc.edu <mailto:genome-mirror%25252Bun...@soe.ucsc.edu>>> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu> <mailto:genome-mirror%252Buns...@soe.ucsc.edu <mailto:genome-mirror%25252Bun...@soe.ucsc.edu>> <mailto:genome-mirror%252Buns...@soe.ucsc.edu <mailto:genome-mirror%25252Bun...@soe.ucsc.edu> <mailto:genome-mirror%25252Bun...@soe.ucsc.edu <mailto:genome-mirror%2525252Bu...@soe.ucsc.edu>>>>.
> > > > >>>>>> .
> > > > >>>>>>
> > > > >>>>>
> > > > >>>>
> > > > >>>> --
> > > > >>>>
> > > > >>>> ---
> > > > >>>> You received this message because you are subscribed to the Google Groups
> > > > >>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > > > >>>> To unsubscribe from this group and stop receiving emails from it, send an
> > > > >>>> To view this discussion on the web visit
> > > > >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu
> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu>>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu
> > > > >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu
> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu>>>>
> > > > >>>> .
> > > > >>>>
> > > > >>>
> > > >
> > > > --
> > > > David Hoover, Ph.D.
> > > > Computational Biologist
> > > > High Performance Computing Services,
> > > > Center for Information Technology,
> > > > National Institutes of Health
> > > > 12 South Dr., Rm 2N207
> > > > Bethesda, MD 20892, USA
> > > > TEL: (+1) 301-435-2986
> > > > Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>>>
> > > > >>>> .
> > > > >>>>
> > > > >>>
> > > >
> > > > --
> > > > David Hoover, Ph.D.
> > > > Computational Biologist
> > > > High Performance Computing Services,
> > > > Center for Information Technology,
> > > > National Institutes of Health
> > > > 12 South Dr., Rm 2N207
> > > > Bethesda, MD 20892, USA
> > > > TEL: (+1) 301-435-2986
> > > >
> > > > --
> > > >
> > > > ---
> > > > You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> > > > To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu>> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu> <mailto:genome-mirror%252Buns...@soe.ucsc.edu <mailto:genome-mirror%25252Bun...@soe.ucsc.edu>>> <mailto:genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu>> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu> <mailto:genome-mirror%252Buns...@soe.ucsc.edu <mailto:genome-mirror%25252Bun...@soe.ucsc.edu>>>>.
> > > > --
> > > >
> > > > ---
> > > > You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> > > > To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com>
> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com>>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com?utm_medium=email&utm_source=footer <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com?utm_medium=email&utm_source=footer> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com?utm_medium=email&utm_source=footer <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com?utm_medium=email&utm_source=footer>>
> > <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com?utm_medium=email&utm_source=footer <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com?utm_medium=email&utm_source=footer> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com?utm_medium=email&utm_source=footer <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com?utm_medium=email&utm_source=footer>>>>.
> > >
> > > --
> > > David Hoover, Ph.D.
> > > Computational Biologist
> > > High Performance Computing Services,
> > > Center for Information Technology,
> > > National Institutes of Health
> > > 12 South Dr., Rm 2N207
> > > Bethesda, MD 20892, USA
> > > TEL: (+1) 301-435-2986
> > > Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>>
> > >
> > > --
> > >
> > > ---
> > > You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> > > To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu>> <mailto:genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu>>>.
> > > To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fy8z%2B%3DmSyDipxamf4P5CFP1YTO_kFyrBW5B-CO%3DHxSQ4A%40mail.gmail.com <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fy8z%2B%3DmSyDipxamf4P5CFP1YTO_kFyrBW5B-CO%3DHxSQ4A%40mail.gmail.com> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fy8z%2B%3DmSyDipxamf4P5CFP1YTO_kFyrBW5B-CO%3DHxSQ4A%40mail.gmail.com <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fy8z%2B%3DmSyDipxamf4P5CFP1YTO_kFyrBW5B-CO%3DHxSQ4A%40mail.gmail.com>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fy8z%2B%3DmSyDipxamf4P5CFP1YTO_kFyrBW5B-CO%3DHxSQ4A%40mail.gmail.com?utm_medium=email&utm_source=footer <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fy8z%2B%3DmSyDipxamf4P5CFP1YTO_kFyrBW5B-CO%3DHxSQ4A%40mail.gmail.com?utm_medium=email&utm_source=footer>
> > <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com?utm_medium=email&utm_source=footer <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com?utm_medium=email&utm_source=footer> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com?utm_medium=email&utm_source=footer <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com?utm_medium=email&utm_source=footer>>>>.
> > >
> > > --
> > > David Hoover, Ph.D.
> > > Computational Biologist
> > > High Performance Computing Services,
> > > Center for Information Technology,
> > > National Institutes of Health
> > > 12 South Dr., Rm 2N207
> > > Bethesda, MD 20892, USA
> > > TEL: (+1) 301-435-2986
> > > Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>>
> > >
> > > --
> > >
> > > ---
> > > You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> > > To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu>> <mailto:genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu>>>.
> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fy8z%2B%3DmSyDipxamf4P5CFP1YTO_kFyrBW5B-CO%3DHxSQ4A%40mail.gmail.com?utm_medium=email&utm_source=footer <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fy8z%2B%3DmSyDipxamf4P5CFP1YTO_kFyrBW5B-CO%3DHxSQ4A%40mail.gmail.com?utm_medium=email&utm_source=footer>>>.
> >
> > --
> > David Hoover, Ph.D.
> > Computational Biologist
> > High Performance Computing Services,
> > Center for Information Technology,
> > National Institutes of Health
> > 12 South Dr., Rm 2N207
> > Bethesda, MD 20892, USA
> > TEL: (+1) 301-435-2986
> > Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>
> >
> > --
> > David Hoover, Ph.D.
> > Computational Biologist
> > High Performance Computing Services,
> > Center for Information Technology,
> > National Institutes of Health
> > 12 South Dr., Rm 2N207
> > Bethesda, MD 20892, USA
> > TEL: (+1) 301-435-2986
> >
> > --
> >
> > ---
> > You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
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> > To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu>>.
> > To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fyDkZxajzBM16-kWe2yb3csonjtL%3DCQR%3DmrcCPc2thrXA%40mail.gmail.com <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fyDkZxajzBM16-kWe2yb3csonjtL%3DCQR%3DmrcCPc2thrXA%40mail.gmail.com> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fyDkZxajzBM16-kWe2yb3csonjtL%3DCQR%3DmrcCPc2thrXA%40mail.gmail.com?utm_medium=email&utm_source=footer <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fyDkZxajzBM16-kWe2yb3csonjtL%3DCQR%3DmrcCPc2thrXA%40mail.gmail.com?utm_medium=email&utm_source=footer>>.
>
> --
> David Hoover, Ph.D.
> Computational Biologist
> High Performance Computing Services,
> Center for Information Technology,
> National Institutes of Health
> 12 South Dr., Rm 2N207
> Bethesda, MD 20892, USA
> TEL: (+1) 301-435-2986
> --
> David Hoover, Ph.D.
> Computational Biologist
> High Performance Computing Services,
> Center for Information Technology,
> National Institutes of Health
> 12 South Dr., Rm 2N207
> Bethesda, MD 20892, USA
> TEL: (+1) 301-435-2986
> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>
>
> --
>
> ---
> You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu>.
> To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/100da894-8997-2d52-d9df-ff1a878f49c5%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/100da894-8997-2d52-d9df-ff1a878f49c5%40hpc.nih.gov>.
>
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> To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu>.
Maximilian Haeussler
Feb 13, 2024, 12:11:37 PM2/13/24
to Hoover, David (NIH/CIT) [E], genome...@soe.ucsc.edu
Hi David,
great!
this has to do with the cookies... but I don't think I've ever had this problem before. Hmm. Can you try removing the trailing "/" from the browserAddr?
To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/100da894-8997-2d52-d9df-ff1a878f49c5%40hpc.nih.gov.
Hoover, David (NIH/CIT) [E]
Mar 21, 2024, 12:19:38 PM3/21/24
to genome...@soe.ucsc.edu
Hi all,
This problem is not going away. We created a VM using rocky9, rather than rocky8, and again I am seeing random lags resulting in timeouts when trying to access remote data via hgTracks.
Can you explain how the GB accesses data from remote servers? What GB libraries or subroutines is it using?
David
This problem is not going away. We created a VM using rocky9, rather than rocky8, and again I am seeing random lags resulting in timeouts when trying to access remote data via hgTracks.
Can you explain how the GB accesses data from remote servers? What GB libraries or subroutines is it using?
David
Maximilian Haeussler
Mar 25, 2024, 1:03:53 PM3/25/24
to Hoover, David (NIH/CIT) [E], genome...@soe.ucsc.edu
Hi David,
hmmm, how can we debug this... As I mentioned, when I tried our prebuilt-binaries in a rocky 9 VM, and even when I built the browser in this VM on rocky 9, it worked fine.
Can you make a tarball from your VM file (VMWare? VirtualBox? something else?) and send it to me? I can try to run your VM here and see if I can reproduce the problem. Once we have this problem reproduced, I am pretty sure that we have a better idea what's going on.
> Can you explain how the GB accesses data from remote servers? What GB libraries or subroutines is it using?
It reads data over the network, but keeps pieces that were read locally in the udcCache directory.
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Hoover, David (NIH/CIT) [E]
May 29, 2025, 12:27:46 PMMay 29
to genome...@soe.ucsc.edu
Hi all,
I just built a docker container using the standard procedure for v482 and the executables were compatible with the OS of the container. I guess whatever changes were implemented fixed our problem. I haven't tried Max's "mirror" & "dev" trick yet, I merely used the generic "install" command.
However... another issue arose. When I compile the utilities for local use on our cluster, the builds got stuck trying to access curl functions:
/usr/local/GCC/11.3.0/bin/gcc -O -g -lcurl -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htsl
ib -I/usr/include/freetype2 -I/usr/include/libpng16 -DUSE_FREETYPE -I/usr/include/libpng16 -o edwQaWigSpotFromRa.o -c edwQaWigSpotFromRa.c
/usr/local/GCC/11.3.0/lib/gcc/x86_64-redhat-linux/11.3.0/../../../../x86_64-redhat-linux/bin/ld: ../../../lib/x86_64/jkhgap.a(cart.o): in function `curlPostUrl':
/lscratch/58449581/kent/src/hg/lib/cart.c:1480: undefined reference to `curl_easy_init'
/usr/local/GCC/11.3.0/lib/gcc/x86_64-redhat-linux/11.3.0/../../../../x86_64-redhat-linux/bin/ld: /lscratch/58449581/kent/src/hg/lib/cart.c:1487: undefined reference to `curl_easy_setopt'
/usr/local/GCC/11.3.0/lib/gcc/x86_64-redhat-linux/11.3.0/../../../../x86_64-redhat-linux/bin/ld: /lscratch/58449581/kent/src/hg/lib/cart.c:1488: undefined reference to `curl_easy_setopt'
/usr/local/GCC/11.3.0/lib/gcc/x86_64-redhat-linux/11.3.0/../../../../x86_64-redhat-linux/bin/ld: /lscratch/58449581/kent/src/hg/lib/cart.c:1489: undefined reference to `curl_easy_setopt'
/usr/local/GCC/11.3.0/lib/gcc/x86_64-redhat-linux/11.3.0/../../../../x86_64-redhat-linux/bin/ld: /lscratch/58449581/kent/src/hg/lib/cart.c:1490: undefined reference to `curl_easy_setopt'
/usr/local/GCC/11.3.0/lib/gcc/x86_64-redhat-linux/11.3.0/../../../../x86_64-redhat-linux/bin/ld: /lscratch/58449581/kent/src/hg/lib/cart.c:1491: undefined reference to `curl_easy_perform'
/usr/local/GCC/11.3.0/lib/gcc/x86_64-redhat-linux/11.3.0/../../../../x86_64-redhat-linux/bin/ld: /lscratch/58449581/kent/src/hg/lib/cart.c:1492: undefined reference to `curl_easy_cleanup'
collect2: error: ld returned 1 exit status
I found a workaround by including -lcurl in the following files:
kent/src/inc/common.mk
kent/src/inc/userApp.mk
kent/src/hg/orthoMap/makefile
I had hoped setting CFLAGS=-lcurl would have worked, but CFLAGS is not universally propagated throughout the build stack. The last two makefiles used COPT and COPTS rather than CFLAGS for extra gcc flags. I don't know exactly why we specifically need -lcurl to enable the curl libraries.
Anyhow, we are now happily using v482. Thanks for all you guys do.
David
On 2/5/2024 11:22 AM, 'Maximilian Haeussler' via UCSC Genome Browser Mirror-Specific Support wrote:
> Hi David,
>
> > https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions>>
> >
> > How up to date is the Docker procedure for the Genome Browser? How difficult would it be to create and use a docker image of the Genome Browser that does not have mysql running internally? We have a substantial mariadb server already full with UCSC data and constantly updated, as well as lots of users' custom tracks. The instructions at https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions>> are very generic and would need to be elaborated to accommodate our local mirror.
> > >>>>>> genome.ucsc.edu <http://genome.ucsc.edu> <http://genome.ucsc.edu <http://genome.ucsc.edu>>
> > >>>>>>>>>>> Genome Browser Mirror-Specific Support <genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu> <mailto:genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu>>
> > >>>>>>>>>>>> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>
> > To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com?utm_medium=email&utm_source=footer <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com?utm_medium=email&utm_source=footer>>.
--
David Hoover, Ph.D.
Computational Biologist
CIT SCS HPCS
Email: david....@nih.gov
I just built a docker container using the standard procedure for v482 and the executables were compatible with the OS of the container. I guess whatever changes were implemented fixed our problem. I haven't tried Max's "mirror" & "dev" trick yet, I merely used the generic "install" command.
However... another issue arose. When I compile the utilities for local use on our cluster, the builds got stuck trying to access curl functions:
/usr/local/GCC/11.3.0/bin/gcc -O -g -lcurl -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htsl
ib -I/usr/include/freetype2 -I/usr/include/libpng16 -DUSE_FREETYPE -I/usr/include/libpng16 -o edwQaWigSpotFromRa.o -c edwQaWigSpotFromRa.c
/usr/local/GCC/11.3.0/lib/gcc/x86_64-redhat-linux/11.3.0/../../../../x86_64-redhat-linux/bin/ld: ../../../lib/x86_64/jkhgap.a(cart.o): in function `curlPostUrl':
/lscratch/58449581/kent/src/hg/lib/cart.c:1480: undefined reference to `curl_easy_init'
/usr/local/GCC/11.3.0/lib/gcc/x86_64-redhat-linux/11.3.0/../../../../x86_64-redhat-linux/bin/ld: /lscratch/58449581/kent/src/hg/lib/cart.c:1487: undefined reference to `curl_easy_setopt'
/usr/local/GCC/11.3.0/lib/gcc/x86_64-redhat-linux/11.3.0/../../../../x86_64-redhat-linux/bin/ld: /lscratch/58449581/kent/src/hg/lib/cart.c:1488: undefined reference to `curl_easy_setopt'
/usr/local/GCC/11.3.0/lib/gcc/x86_64-redhat-linux/11.3.0/../../../../x86_64-redhat-linux/bin/ld: /lscratch/58449581/kent/src/hg/lib/cart.c:1489: undefined reference to `curl_easy_setopt'
/usr/local/GCC/11.3.0/lib/gcc/x86_64-redhat-linux/11.3.0/../../../../x86_64-redhat-linux/bin/ld: /lscratch/58449581/kent/src/hg/lib/cart.c:1490: undefined reference to `curl_easy_setopt'
/usr/local/GCC/11.3.0/lib/gcc/x86_64-redhat-linux/11.3.0/../../../../x86_64-redhat-linux/bin/ld: /lscratch/58449581/kent/src/hg/lib/cart.c:1491: undefined reference to `curl_easy_perform'
/usr/local/GCC/11.3.0/lib/gcc/x86_64-redhat-linux/11.3.0/../../../../x86_64-redhat-linux/bin/ld: /lscratch/58449581/kent/src/hg/lib/cart.c:1492: undefined reference to `curl_easy_cleanup'
collect2: error: ld returned 1 exit status
I found a workaround by including -lcurl in the following files:
kent/src/inc/common.mk
kent/src/inc/userApp.mk
kent/src/hg/orthoMap/makefile
I had hoped setting CFLAGS=-lcurl would have worked, but CFLAGS is not universally propagated throughout the build stack. The last two makefiles used COPT and COPTS rather than CFLAGS for extra gcc flags. I don't know exactly why we specifically need -lcurl to enable the curl libraries.
Anyhow, we are now happily using v482. Thanks for all you guys do.
David
On 2/5/2024 11:22 AM, 'Maximilian Haeussler' via UCSC Genome Browser Mirror-Specific Support wrote:
> Hi David,
>
> OK, I've spent time on this, but still can't reproduce it:
>
> (1) Took an empty Rocky 8 VM on my laptop, installed and built the CGIs there, but can access hubs just fine. I'm not getting the error that you saw. I tried the Alfa hub, as this is also on the NIH campus:
> https://ftp.ncbi.nlm.nih.gov/snp/population_frequency/TrackHub/latest/hub.txt <https://ftp.ncbi.nlm.nih.gov/snp/population_frequency/TrackHub/latest/hub.txt>. It displays without errors...
>
> (1) Took an empty Rocky 8 VM on my laptop, installed and built the CGIs there, but can access hubs just fine. I'm not getting the error that you saw. I tried the Alfa hub, as this is also on the NIH campus:
>
> (2) So I added a command "dev" to our installation script. If you run this after the "mirror" command, it will install all requirements, clone the git repo and build all the CGIs from scratch. This should help you build the CGIs yourself in a fresh VM or Docker container and may also help us track down problems: you can now compare the (pretty simple) yum and make commands in that script with what you use. For example, there is no static linking with any dependencies if you look at the linker command (see below).
> Here is the version of the script with the "dev" command, it will soon land on github but I am sending you a link right now so you can test it:
> https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh <https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh>
> (2) So I added a command "dev" to our installation script. If you run this after the "mirror" command, it will install all requirements, clone the git repo and build all the CGIs from scratch. This should help you build the CGIs yourself in a fresh VM or Docker container and may also help us track down problems: you can now compare the (pretty simple) yum and make commands in that script with what you use. For example, there is no static linking with any dependencies if you look at the linker command (see below).
> Here is the version of the script with the "dev" command, it will soon land on github but I am sending you a link right now so you can test it:
>
> On a fresh VM or Docker container, you should be able to run these three commands to make a browser mirror and build everything:
>
> wget https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh <https://hgwdev.gi.ucsc.edu/~max/davidHoover/browserSetup.sh>
> On a fresh VM or Docker container, you should be able to run these three commands to make a browser mirror and build everything:
>
> > Can you elaborate what you mean with "accommodate our local mirror" ?
> >
> > I just tried an Ubuntu 22 a few days ago and ran the browserSetup.sh script in it and it just worked. I didn't use the docker commands, ran the browserSetup.sh -b install manually but I had a working mirror 2 minutes later.
> >
> > I wanted to try Rocky 8 next and unfortunately got distracted by grant reviews...
> >
> >
> >
> > On Mon, Jan 29, 2024 at 3:38 PM Hoover, David (NIH/CIT) [E] <hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>> wrote:
> >
> > I just tried an Ubuntu 22 a few days ago and ran the browserSetup.sh script in it and it just worked. I didn't use the docker commands, ran the browserSetup.sh -b install manually but I had a working mirror 2 minutes later.
> >
> > I wanted to try Rocky 8 next and unfortunately got distracted by grant reviews...
> >
> >
> >
> >
> > How up to date is the Docker procedure for the Genome Browser? How difficult would it be to create and use a docker image of the Genome Browser that does not have mysql running internally? We have a substantial mariadb server already full with UCSC data and constantly updated, as well as lots of users' custom tracks. The instructions at https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions> <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions <https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions>> are very generic and would need to be elaborated to accommodate our local mirror.
> >
> > David
> >
> > On 1/22/2024 2:44 PM, Christopher Lee wrote:
> > > Hi Belinda and David,
> > >
> > > Unfortunately we are just completely stumped on what is going on here,
> > > and we do not have the resources to continue looking further. The only
> > > thing we can say is that we ourselves are upgrading to Rocky 9 soon
> > > and have verified at least minimal function with that operating
> > > system, so you can try upgrading and see if that fixes the problem.
> > >
> > > As far as theories, we suspect that somehow the MySQL/MariaDb
> > > installation could be misconfigured, even though that seemed to have
> > > been ruled out already.
> > >
> > > If you do find the cause of the problem and/or a fix, we would of
> > > course love to hear about it and accept a pull request or fix.
> > >
> > > Thanks,
> > > Christopher Lee
> > > UCSC Genomics Institute
> > >
> > > On Tue, Jan 16, 2024 at 12:07 PM Belinda M. Giardine
> > David
> >
> > On 1/22/2024 2:44 PM, Christopher Lee wrote:
> > > Hi Belinda and David,
> > >
> > > Unfortunately we are just completely stumped on what is going on here,
> > > and we do not have the resources to continue looking further. The only
> > > thing we can say is that we ourselves are upgrading to Rocky 9 soon
> > > and have verified at least minimal function with that operating
> > > system, so you can try upgrading and see if that fixes the problem.
> > >
> > > As far as theories, we suspect that somehow the MySQL/MariaDb
> > > installation could be misconfigured, even though that seemed to have
> > > been ruled out already.
> > >
> > > If you do find the cause of the problem and/or a fix, we would of
> > > course love to hear about it and accept a pull request or fix.
> > >
> > > Thanks,
> > > Christopher Lee
> > > UCSC Genomics Institute
> > >
> > > On Tue, Jan 16, 2024 at 12:07 PM Belinda M. Giardine
> > > <giar...@bx.psu.edu <mailto:giar...@bx.psu.edu> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>>> wrote:
> > >>
> > >> I put a copy of the files in the cgi-bin here
> > >> https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/ <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/> <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/ <https://www.bx.psu.edu/~giardine/tests/tmp/ucsc_cgis/>>
> > >>
> > >> I put a copy of the files in the cgi-bin here
> > >>
> > >> If you mean you want to be able to access the pages on our server the
> > >> public version is
> > >> https://main.genome-browser.bx.psu.edu/ <https://main.genome-browser.bx.psu.edu/> <https://main.genome-browser.bx.psu.edu/ <https://main.genome-browser.bx.psu.edu/>>
> > >> If you mean you want to be able to access the pages on our server the
> > >> public version is
> > >>
> > >> Belinda
> > >>
> > >>
> > >> On Tue, 16 Jan 2024, Jairo Navarro Gonzalez wrote:
> > >>
> > >>> Hello,
> > >>>
> > >>> Thank you for using the UCSC Genome Browser and reporting your issues.
> > >>>
> > >>> Would it be possible to place the binaries in a web-accessible location?
> > >>> This way, our engineers can have a reproducible case to debug the issue.
> > >>>
> > >>> If you have any further questions, please reply to gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu> <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>>.
> > >> Belinda
> > >>
> > >>
> > >> On Tue, 16 Jan 2024, Jairo Navarro Gonzalez wrote:
> > >>
> > >>> Hello,
> > >>>
> > >>> Thank you for using the UCSC Genome Browser and reporting your issues.
> > >>>
> > >>> Would it be possible to place the binaries in a web-accessible location?
> > >>> This way, our engineers can have a reproducible case to debug the issue.
> > >>>
> > >>> All messages sent to that address are archived on a publicly accessible
> > >>> Google Groups forum.
> > >>> If your question includes sensitive data, you may send it instead to
> > >>> genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu> <mailto:genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>>.
> > >>> Google Groups forum.
> > >>> If your question includes sensitive data, you may send it instead to
> > >>>
> > >>> Jairo Navarro
> > >>> UCSC Genome Browser
> > >>>
> > >>> On Tue, Jan 2, 2024 at 8:56?AM Belinda M. Giardine <giar...@bx.psu.edu <mailto:giar...@bx.psu.edu> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>>>
> > >>> Jairo Navarro
> > >>> UCSC Genome Browser
> > >>>
> > >>> wrote:
> > >>>
> > >>>> We are building our own binaries. It is running on a VM.
> > >>>>
> > >>>> Belinda
> > >>>>
> > >>>>
> > >>>> On Fri, 22 Dec 2023, Maximilian Haeussler wrote:
> > >>>>
> > >>>>> David and Belinda,
> > >>>>> thank you for your patience with this, it's hard to debug if we don't
> > >>>> have
> > >>>>> access to a machine and can't reproduce the problem. We don't think it's
> > >>>>> Rocky 9 itself (trying with a VM).
> > >>>>> Are you both building your own binaries from the source code or are you
> > >>>>> using our pre-built binaries?
> > >>>>> thanks
> > >>>>> Max
> > >>>>>
> > >>>>> On Mon, Dec 18, 2023 at 8:31?PM Belinda M. Giardine <giar...@bx.psu.edu <mailto:giar...@bx.psu.edu> <mailto:giar...@bx.psu.edu <mailto:giar...@bx.psu.edu>>
> > >>>
> > >>>> We are building our own binaries. It is running on a VM.
> > >>>>
> > >>>> Belinda
> > >>>>
> > >>>>
> > >>>> On Fri, 22 Dec 2023, Maximilian Haeussler wrote:
> > >>>>
> > >>>>> David and Belinda,
> > >>>>> thank you for your patience with this, it's hard to debug if we don't
> > >>>> have
> > >>>>> access to a machine and can't reproduce the problem. We don't think it's
> > >>>>> Rocky 9 itself (trying with a VM).
> > >>>>> Are you both building your own binaries from the source code or are you
> > >>>>> using our pre-built binaries?
> > >>>>> thanks
> > >>>>> Max
> > >>>>>
> > >>>>>
> > >>>>>>>>>>> wrote:
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> Now I am not so sure what is happening.? Here are some
> > >>>> observations:
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> * The timeout issue holds not just for custom tracks, for the
> > >>>> track
> > >>>>>>>>>>>> hubs as well
> > >>>>>>>>>>>> * On the UCSC site, I can load tracks and a hub hosted on our
> > >>>> local
> > >>>>>>>>>>>> dataserver (hpc.nih.gov <http://hpc.nih.gov> <http://hpc.nih.gov <http://hpc.nih.gov>>), and these display normally
> > >>>>>>>>>>> wrote:
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> Now I am not so sure what is happening.? Here are some
> > >>>> observations:
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> * The timeout issue holds not just for custom tracks, for the
> > >>>> track
> > >>>>>>>>>>>> hubs as well
> > >>>>>>>>>>>> * On the UCSC site, I can load tracks and a hub hosted on our
> > >>>> local
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> --
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> ---
> > >>>>>>>>>>>> You received this message because you are subscribed to the Google
> > >>>>>>>>>>>> Groups "UCSC Genome Browser Mirror-Specific Support" group.
> > >>>>>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
> > >>>>>> send
> > >>>>>>>>>>>> an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu>>.
> > >>>>>>>>>>>> --
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> ---
> > >>>>>>>>>>>> You received this message because you are subscribed to the Google
> > >>>>>>>>>>>> Groups "UCSC Genome Browser Mirror-Specific Support" group.
> > >>>>>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
> > >>>>>> send
> > >>>>>>>>>>>> To view this discussion on the web visit
> > >>>>>>>>>>>>
> > >>>>>>
> > >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/88325cba-ecc8-489d-bfbd-f9ed7f97ddc7%40hpc.nih.gov>>
> > >>>>>>>>>>>>
> > >>>>>>
> > >>>>>> .
> > >>>>>>>>>>>
> > >>>>>>>>>
> > >>>>>>>>> --
> > >>>>>>>>> David Hoover, Ph.D.
> > >>>>>>>>> Computational Biologist
> > >>>>>>>>> High Performance Computing Services,
> > >>>>>>>>> Center for Information Technology,
> > >>>>>>>>> National Institutes of Health
> > >>>>>>>>> 12 South Dr., Rm 2N207
> > >>>>>>>>> Bethesda, MD 20892, USA
> > >>>>>>>>> TEL: (+1) 301-435-2986
> > >>>>>>>>> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>
> > >>>>>>>>>>>
> > >>>>>>>>>
> > >>>>>>>>> --
> > >>>>>>>>> David Hoover, Ph.D.
> > >>>>>>>>> Computational Biologist
> > >>>>>>>>> High Performance Computing Services,
> > >>>>>>>>> Center for Information Technology,
> > >>>>>>>>> National Institutes of Health
> > >>>>>>>>> 12 South Dr., Rm 2N207
> > >>>>>>>>> Bethesda, MD 20892, USA
> > >>>>>>>>> TEL: (+1) 301-435-2986
> > >>>>>>>>>
> > >>>>>>>>> --
> > >>>>>>>>>
> > >>>>>>>>> ---
> > >>>>>>>>> You received this message because you are subscribed to the Google
> > >>>>>> Groups
> > >>>>>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > >>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
> > >>>> send
> > >>>>>> an
> > >>>>>>>>> email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu>>.
> > >>>>>>>>> --
> > >>>>>>>>>
> > >>>>>>>>> ---
> > >>>>>>>>> You received this message because you are subscribed to the Google
> > >>>>>> Groups
> > >>>>>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > >>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
> > >>>> send
> > >>>>>> an
> > >>>>>>>>> To view this discussion on the web visit
> > >>>>>>>>>
> > >>>>>>
> > >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/afd2916f-4681-4426-21f4-ddb5405fecfc%40hpc.nih.gov>>
> > >>>>>>>>>
> > >>>>>>
> > >>>>>> .
> > >>>>>>>
> > >>>>>>> --
> > >>>>>>> David Hoover, Ph.D.
> > >>>>>>> Computational Biologist
> > >>>>>>> High Performance Computing Services,
> > >>>>>>> Center for Information Technology,
> > >>>>>>> National Institutes of Health
> > >>>>>>> 12 South Dr., Rm 2N207
> > >>>>>>> Bethesda, MD 20892, USA
> > >>>>>>> TEL: (+1) 301-435-2986
> > >>>>>>> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>
> > >>>>>>>
> > >>>>>>> --
> > >>>>>>> David Hoover, Ph.D.
> > >>>>>>> Computational Biologist
> > >>>>>>> High Performance Computing Services,
> > >>>>>>> Center for Information Technology,
> > >>>>>>> National Institutes of Health
> > >>>>>>> 12 South Dr., Rm 2N207
> > >>>>>>> Bethesda, MD 20892, USA
> > >>>>>>> TEL: (+1) 301-435-2986
> > >>>>>>>
> > >>>>>>> --
> > >>>>>>>
> > >>>>>>> --- You received this message because you are subscribed to the Google
> > >>>>>> Groups
> > >>>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > >>>>>>> To unsubscribe from this group and stop receiving emails from it, send
> > >>>>>> an
> > >>>>>>> email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu>>.
> > >>>>>>> --
> > >>>>>>>
> > >>>>>>> --- You received this message because you are subscribed to the Google
> > >>>>>> Groups
> > >>>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > >>>>>>> To unsubscribe from this group and stop receiving emails from it, send
> > >>>>>> an
> > >>>>>>> To view this discussion on the web visit
> > >>>>>>>
> > >>>>>>
> > >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5cd7a537-2f76-05bb-f779-ddc8807fae7b%40hpc.nih.gov>>
> > >>>>>>>
> > >>>>>>
> > >>>>>> .
> > >>>>>>>
> > >>>>>>>
> > >>>>>>
> > >>>>>> --
> > >>>>>>
> > >>>>>> ---
> > >>>>>> You received this message because you are subscribed to the Google
> > >>>> Groups
> > >>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > >>>>>> To unsubscribe from this group and stop receiving emails from it, send
> > >>>> an
> > >>>>>> email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu>>.
> > >>>>>>>
> > >>>>>>>
> > >>>>>>
> > >>>>>> --
> > >>>>>>
> > >>>>>> ---
> > >>>>>> You received this message because you are subscribed to the Google
> > >>>> Groups
> > >>>>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > >>>>>> To unsubscribe from this group and stop receiving emails from it, send
> > >>>> an
> > >>>>>> To view this discussion on the web visit
> > >>>>>>
> > >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2312181326170.20267%40uniport.bx.psu.edu>>
> > >>>>>>
> > >>>>>> .
> > >>>>>>
> > >>>>>
> > >>>>
> > >>>> --
> > >>>>
> > >>>> ---
> > >>>> You received this message because you are subscribed to the Google Groups
> > >>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > >>>> To unsubscribe from this group and stop receiving emails from it, send an
> > >>>> email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu <mailto:genome-mirror%252Buns...@soe.ucsc.edu>>.
> > >>>>>>
> > >>>>>
> > >>>>
> > >>>> --
> > >>>>
> > >>>> ---
> > >>>> You received this message because you are subscribed to the Google Groups
> > >>>> "UCSC Genome Browser Mirror-Specific Support" group.
> > >>>> To unsubscribe from this group and stop receiving emails from it, send an
> > >>>> To view this discussion on the web visit
> > >>>> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/alpine.DEB.2.21.2401021122170.4445%40uniport.bx.psu.edu>>
> > >>>> .
> > >>>>
> > >>>
> >
> > --
> > David Hoover, Ph.D.
> > Computational Biologist
> > High Performance Computing Services,
> > Center for Information Technology,
> > National Institutes of Health
> > 12 South Dr., Rm 2N207
> > Bethesda, MD 20892, USA
> > TEL: (+1) 301-435-2986
> > Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov> <mailto:hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>>
> > >>>>
> > >>>
> >
> > --
> > David Hoover, Ph.D.
> > Computational Biologist
> > High Performance Computing Services,
> > Center for Information Technology,
> > National Institutes of Health
> > 12 South Dr., Rm 2N207
> > Bethesda, MD 20892, USA
> > TEL: (+1) 301-435-2986
> >
> > --
> >
> > ---
> > You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> > To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu> <mailto:genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu>>.
> > --
> >
> > ---
> > You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> > To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com?utm_medium=email&utm_source=footer <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fxAe8kdOXWy4QUihp1V0LdUuBBBPW4cOiRf0TzuSE4%3D_g%40mail.gmail.com?utm_medium=email&utm_source=footer>>.
>
> --
> David Hoover, Ph.D.
> Computational Biologist
> High Performance Computing Services,
> Center for Information Technology,
> National Institutes of Health
> 12 South Dr., Rm 2N207
> Bethesda, MD 20892, USA
> TEL: (+1) 301-435-2986
> --
> David Hoover, Ph.D.
> Computational Biologist
> High Performance Computing Services,
> Center for Information Technology,
> National Institutes of Health
> 12 South Dr., Rm 2N207
> Bethesda, MD 20892, USA
> TEL: (+1) 301-435-2986
> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>
>
> --
>
> ---
> You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirro...@soe.ucsc.edu>.
> To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fy8z%2B%3DmSyDipxamf4P5CFP1YTO_kFyrBW5B-CO%3DHxSQ4A%40mail.gmail.com <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/CAHm%3D4fy8z%2B%3DmSyDipxamf4P5CFP1YTO_kFyrBW5B-CO%3DHxSQ4A%40mail.gmail.com?utm_medium=email&utm_source=footer>.
>
> --
>
> ---
> You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirro...@soe.ucsc.edu>.
--
David Hoover, Ph.D.
Computational Biologist
National Institutes of Health
12 South Dr., Rm 2N207
TEL: (+1) 301-435-2986
12 South Dr., Rm 2N207
Email: david....@nih.gov
Maximilian Haeussler
Jun 2, 2025, 12:58:24 PMJun 2
to Hoover, David (NIH/CIT) [E], genome...@soe.ucsc.edu
Hi David,
hmm, I think you used the master branch, is that correct? If so, this is probably my fault.
best
Max
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