Refresh the hubs

[Sukhdeep Singh]

Hi,
I have overlayed multiple bigwig files using track hubs, great.

The problem is the refresh limit, whatever I add to my trackDB file, the main
hub in the browser shows after long time(~5-10 mins), even If I reset the
browser https://genome.ucsc.edu/cgi-bin/cartReset
or delete the hub from my hubs genome.ucsc.edu/cgi-bin/hgHubConnect?
hubId=20771&hgHub_do_disconnect=on&hgHubConnect.remakeTrackHub=on.


How can I make it faster, is the lag at my server or yours.
Here's my hub link : https://projects.biotec.tu-
dresden.de/sukhdeeps_webdav/multiWig/hubs/bod1LmarksHub.txt

When I use hubcheck with the above link, the error is
No openssl available in netConnectHttps for projects.biotec.tu-dresden.de :
443

Another problem is, how many containers can I define in my trackDB file, I
have 2 containers with 3 bigwigs each, but when I scale up to 4 container,
the genome browser just loads the header with assembly name and genomic co-
ordinates but the tracks are empty.

Thanks

[Matthew Speir]

Hi Sukhdeep,

Thank you for your questions about tracks hubs. The UCSC hub utility caches your files on our servers, and it will periodically (~300 seconds) compare the time stamps of those files on our server with those on yours. If the time stamps of the files on your server are newer, then it will update those cached files on our server. This means that it can take up to 5 minutes between when you change the files on your server, and when you see those changes in the browser. The debug section of our Track Hub user guide, http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Debug, contains information on how to reduce this delay time.

There are a few other issues with your hub. When one of our engineers ran hubCheck on your hub, they got the following results:

    hubCheck -udcDir=$HOME https://projects.biotec.tu-dresden.de/sukhdeeps_webdav/multiWig/hubs/bod1LmarksHub.txt
    Errors with hub at 'https://projects.biotec.tu-dresden.de/sukhdeeps_webdav/multiWig/hubs/bod1LmarksHub.txt'
    Couldn't open https://projects.biotec.tu-dresden.de/sukhdeeps_webdav/mm10/histoneChips/Bod1L_FKO_H3K4me1_45.bw
    Couldn't open https://projects.biotec.tu-dresden.de/sukhdeeps_webdav/mm10/histoneChips/Bod1L_FKO_H3K4me3_45.bw

When I try to navigate to those files, I get a '404 Not Found'. You should verify that those files are indeed at those locations, or change your trackDb to point to the correct locations. These missing files were also the source of the other problem you were seeing, and were essentially causing the browser to crash when loading your hub. This helped us discover and fix some issues in our code. This fix will be incorporated into a future release of our software, currently scheduled for release on March 4.

Lastly, when running hubCheck the reason you are seeing the openssl error is because the program was compiled without USE_SSL turned on. If you are compiling the userApps from the source, make sure that the Makefile in kent/src/userApps/ contains the line:

    export USE_SSL = 1

We also offer pre-built versions of these utilities for Unix based environments at http://hgdownload.soe.ucsc.edu/admin/exe/.

I hope this is helpful. 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.

Matthew Speir
UCSC Genome Bioinformatics Group