Issues installing local browser
41 views
Skip to first unread message
Sood, Pranidhi
Apr 6, 2016, 5:25:42 PM4/6/16
to genome...@soe.ucsc.edu
Hi —
I have been trying to install a minimal browser locally for our lab. I think I have set up everything properly, but can’t seem to get beyond this error:
The requested URL /cgi-bin/hgGateway was not found on this server.
Looking through the google groups, I realize that this might have something to do with mysql permissions, but as far as I can tell I have set them up properly.
Attached is a screenshot of my home page. I am running Ubuntu 14.04 and Apache2, version 2.4.7.
Thanks very much for any assistance!
Pranidhi
Matthew Speir
Apr 7, 2016, 12:57:13 PM4/7/16
to Sood, Pranidhi, genome...@soe.ucsc.edu
Hi Pranidhi,
Thank you for your question about installing a mirror of the UCSC Genome Browser.
Can you provide more information about what you need the full mirror for? It may be the case that what you're looking to do can be done without needed to install a full mirror.
For example, if you're looking to load a custom set of annotations for a genome we host or even load your own genome and its annotations, you can use a track or assembly hub. Track hubs allow you to load up a custom set of annotations for an organism we host and control the display of these annotations in a way that's similar to native tracks. Assembly hubs expand this and allow you to display your own genomic sequence and its related annotations in the Genome Browser. You can even set up and specify BLAT/isPCR servers for your assembly and use the UCSC web interface for these tools with your custom genome. You can read more about track and assembly hubs in the user guide, http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html.
If you are just looking to have a personal instance of the UCSC Genome Browser in which you can display and navigate your private data, you can use Genome Browser in a Box (GBiB) which is a virtual image of the entire Genome Browser software and related tools that can be used from your personal computer. You can find instructions on downloading and setting up GBiB here: http://genome.ucsc.edu/goldenPath/help/gbib.html.
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
Thank you for your question about installing a mirror of the UCSC Genome Browser.
Can you provide more information about what you need the full mirror for? It may be the case that what you're looking to do can be done without needed to install a full mirror.
For example, if you're looking to load a custom set of annotations for a genome we host or even load your own genome and its annotations, you can use a track or assembly hub. Track hubs allow you to load up a custom set of annotations for an organism we host and control the display of these annotations in a way that's similar to native tracks. Assembly hubs expand this and allow you to display your own genomic sequence and its related annotations in the Genome Browser. You can even set up and specify BLAT/isPCR servers for your assembly and use the UCSC web interface for these tools with your custom genome. You can read more about track and assembly hubs in the user guide, http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html.
If you are just looking to have a personal instance of the UCSC Genome Browser in which you can display and navigate your private data, you can use Genome Browser in a Box (GBiB) which is a virtual image of the entire Genome Browser software and related tools that can be used from your personal computer. You can find instructions on downloading and setting up GBiB here: http://genome.ucsc.edu/goldenPath/help/gbib.html.
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
--
Matthew Speir
Apr 14, 2016, 1:35:29 PM4/14/16
to Sood, Pranidhi, genome...@soe.ucsc.edu
Hi Pranidhi,
Thank you for providing more details about what you're looking to do.
I'm not not sure how much you're looking to keep your unpublished data private and completely unavailable to the outside world, but it may be that using a combination of the GBiB and an assembly hub or just an assembly hub on its own would be sufficient.
Assembly hubs require that your data be placed on a publicly-accessible web server. You provide the URL to your assembly data on this publicly-accessible web server to the UCSC Genome Browser and it will load your assembly and its annotations into the Browser from there. The disadvantage to this being that anyone who has the URL is able to access your assembly and its annotations. I know that others in the past have limited access to the assembly hub data to only the Genome Browser and a select few by limiting access to the hub files based on IP address. The data will still be accessible from the Genome Browser to anyone with the URL to your data, but bulk access to the files will be restricted. Information on creating assembly hubs can be found here: http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html or here: http://genomewiki.ucsc.edu/index.php/Assembly_Hubs.
If the assembly hub on its own provides others too much access to your data, you can use the GBiB plus an assembly hub. This alongside limiting access to the GBiB based on IP address would provide you with more control over who can access the data. While GBiB was designed for use on a personal computer by a single person, however, it should possible to integrate it into a server and allow access from multiple sources. Opening up access to the outside is described here: http://genome.ucsc.edu/goldenPath/help/gbib.html#SharingGBIB. You can then use firewall rules to restrict access to your GBiB instance. Additionally, there's this genomewiki page about integrating assembly hubs into your GBiB instance which should helpful if you decide to go this route: http://genomewiki.ucsc.edu/index.php/GBiB:_From_download_to_BLAT_at_assembly_hubs.
If neither of those options sounds appealing to you and you would like to continue with a full mirror install, I would highly recommend reading through the kent/src/product/README.* files. These files contain the most up-to-date and comprehensive information regarding how to properly install and set up a mirror of the UCSC Genome Browser. You can view these README files on the web here: https://github.com/ucscGenomeBrowser/kent/tree/master/src/product, starting with the README.requirements or README.install files. If you downloaded the full Kent source tree, they should be in the kent/src/product directory.
I hope this is helpful. If you have any further questions, please reply to genome...@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.
Thank you for providing more details about what you're looking to do.
I'm not not sure how much you're looking to keep your unpublished data private and completely unavailable to the outside world, but it may be that using a combination of the GBiB and an assembly hub or just an assembly hub on its own would be sufficient.
Assembly hubs require that your data be placed on a publicly-accessible web server. You provide the URL to your assembly data on this publicly-accessible web server to the UCSC Genome Browser and it will load your assembly and its annotations into the Browser from there. The disadvantage to this being that anyone who has the URL is able to access your assembly and its annotations. I know that others in the past have limited access to the assembly hub data to only the Genome Browser and a select few by limiting access to the hub files based on IP address. The data will still be accessible from the Genome Browser to anyone with the URL to your data, but bulk access to the files will be restricted. Information on creating assembly hubs can be found here: http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html or here: http://genomewiki.ucsc.edu/index.php/Assembly_Hubs.
If the assembly hub on its own provides others too much access to your data, you can use the GBiB plus an assembly hub. This alongside limiting access to the GBiB based on IP address would provide you with more control over who can access the data. While GBiB was designed for use on a personal computer by a single person, however, it should possible to integrate it into a server and allow access from multiple sources. Opening up access to the outside is described here: http://genome.ucsc.edu/goldenPath/help/gbib.html#SharingGBIB. You can then use firewall rules to restrict access to your GBiB instance. Additionally, there's this genomewiki page about integrating assembly hubs into your GBiB instance which should helpful if you decide to go this route: http://genomewiki.ucsc.edu/index.php/GBiB:_From_download_to_BLAT_at_assembly_hubs.
If neither of those options sounds appealing to you and you would like to continue with a full mirror install, I would highly recommend reading through the kent/src/product/README.* files. These files contain the most up-to-date and comprehensive information regarding how to properly install and set up a mirror of the UCSC Genome Browser. You can view these README files on the web here: https://github.com/ucscGenomeBrowser/kent/tree/master/src/product, starting with the README.requirements or README.install files. If you downloaded the full Kent source tree, they should be in the kent/src/product directory.
I hope this is helpful. If you have any further questions, please reply to genome...@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
On 4/7/16 10:18 AM, Sood, Pranidhi
wrote:
Hi Matthew,
Thanks for you fast response!
We have recently sequenced the genome of a non-model organism. My goal is to set up a UCSC genome browser instance just for that genome with tracks for all the additional data that we’ve accumulated. We have a server in the lab which we’d hoped to use as the host for this, so that all of our collaborators could access the data.
The Assembly hub you describe here might be a solution for us, but we have a lot of data (unpublished). It would be nice if we had an instance of the browser where that data was already loaded.
If you have any thoughts, please let me know!
Thanks,Pranidhi
Reply all
Reply to author
Forward
0 new messages