using local Genome Browser mirror
Is there any way of having Galaxy use a local mirror of the UCSC Genome Browser instead of the main site? Is there a central config file somewhere that I can just change genome.ucsc.edu to something else? David Hoover Helix Systems Staff http://helix.nih.gov
Hi David, For the table browser we set up here. [galaxy:tool_runners] biomart = local:/// encode_db1 = local:/// hbvar = local:/// microbial_import1 = local:/// ucsc_table_direct1 = http://localgenome.cgi-bin/hgTables ucsc_table_direct_archaea1 = local:/// ucsc_table_direct_test1 = local:/// upload1 = local:/// For displaying the actual genome with bed files we changed the file. /galaxy-central/tool-data/shared/ucsc So it points to our local genome browser. Hope this helps. Victor On Nov 2, 2010, at 12:23 PM, David Hoover wrote:
Is there any way of having Galaxy use a local mirror of the UCSC Genome Browser instead of the main site? Is there a central config file somewhere that I can just change genome.ucsc.edu to something else?
David Hoover Helix Systems Staff http://helix.nih.gov _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
I modified universe_wsgi.ini and the files in ~/tool-data/shared/ucsc, then restarted galaxy, but it still downloads data from UCSC instead of the local mirror. Is there something I missed? David On Nov 2, 2010, at 1:31 PM, Victor Ruotti wrote: Hi David, For the table browser we set up here. [galaxy:tool_runners] biomart = local:/// encode_db1 = local:/// hbvar = local:/// microbial_import1 = local:/// ucsc_table_direct1 = http://localgenome.cgi-bin/hgTables ucsc_table_direct_archaea1 = local:/// ucsc_table_direct_test1 = local:/// upload1 = local:/// For displaying the actual genome with bed files we changed the file. /galaxy-central/tool-data/shared/ucsc So it points to our local genome browser. Hope this helps. Victor On Nov 2, 2010, at 12:23 PM, David Hoover wrote:
Is there any way of having Galaxy use a local mirror of the UCSC Genome Browser instead of the main site? Is there a central config file somewhere that I can just change genome.ucsc.edu to something else?
David Hoover Helix Systems Staff http://helix.nih.gov _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Hi David, This might help you. http://bitbucket.org/galaxy/galaxy-central/wiki/UCSC2Galaxy Victor On Nov 2, 2010, at 1:10 PM, David Hoover wrote:
I modified universe_wsgi.ini and the files in ~/tool-data/shared/ucsc, then restarted galaxy, but it still downloads data from UCSC instead of the local mirror. Is there something I missed?
David
On Nov 2, 2010, at 1:31 PM, Victor Ruotti wrote:
Hi David, For the table browser we set up here. [galaxy:tool_runners] biomart = local:/// encode_db1 = local:/// hbvar = local:/// microbial_import1 = local:/// ucsc_table_direct1 = http://localgenome.cgi-bin/hgTables ucsc_table_direct_archaea1 = local:/// ucsc_table_direct_test1 = local:/// upload1 = local:///
For displaying the actual genome with bed files we changed the file. /galaxy-central/tool-data/shared/ucsc
So it points to our local genome browser.
Hope this helps. Victor
On Nov 2, 2010, at 12:23 PM, David Hoover wrote:
Is there any way of having Galaxy use a local mirror of the UCSC Genome Browser instead of the main site? Is there a central config file somewhere that I can just change genome.ucsc.edu to something else?
David Hoover Helix Systems Staff http://helix.nih.gov _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Sorry, I see that the link does not work. Or maybe under, /galaxy-central/tools/data_source/ucsc_tablebrowser.xml ? I'm willing to help writing some documentation of this if not already in bitbucket. Victor Victor On Nov 2, 2010, at 1:21 PM, Victor Ruotti wrote:
Hi David, This might help you. http://bitbucket.org/galaxy/galaxy-central/wiki/UCSC2Galaxy
Victor
On Nov 2, 2010, at 1:10 PM, David Hoover wrote:
I modified universe_wsgi.ini and the files in ~/tool-data/shared/ucsc, then restarted galaxy, but it still downloads data from UCSC instead of the local mirror. Is there something I missed?
David
On Nov 2, 2010, at 1:31 PM, Victor Ruotti wrote:
Hi David, For the table browser we set up here. [galaxy:tool_runners] biomart = local:/// encode_db1 = local:/// hbvar = local:/// microbial_import1 = local:/// ucsc_table_direct1 = http://localgenome.cgi-bin/hgTables ucsc_table_direct_archaea1 = local:/// ucsc_table_direct_test1 = local:/// upload1 = local:///
For displaying the actual genome with bed files we changed the file. /galaxy-central/tool-data/shared/ucsc
So it points to our local genome browser.
Hope this helps. Victor
On Nov 2, 2010, at 12:23 PM, David Hoover wrote:
Is there any way of having Galaxy use a local mirror of the UCSC Genome Browser instead of the main site? Is there a central config file somewhere that I can just change genome.ucsc.edu to something else?
David Hoover Helix Systems Staff http://helix.nih.gov _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Victor Ruotti wrote:
Hi David, This might help you. http://bitbucket.org/galaxy/galaxy-central/wiki/UCSC2Galaxy
Sorry, this information is a bit outdated. There is a more recent page that covers writing display applications, but it's written from the perspective of adding entirely new display applications rather than linking to an existing browser: http://bitbucket.org/galaxy/galaxy-central/wiki/ExternalDisplayApplications/... The relevant information is that that the site should be given a name and added to: galaxy_dist/tool-data/shared/ucsc/ucsc_build_sites.txt Once done, that name should be added to the parameter 'ucsc_display_sites' in universe_wsgi.ini. This will enable your browser for the "display at ..." links under compatible file types of data in your history. To add your local mirror as a data source tool, you'll need to make a copy of: galaxy_dist/data_source/ucsc_tablebrowser.xml And change the URL in the <inputs> tag to point to your local browser. Once this is done, add the path to your new XML file to 'tool_conf.xml' and restart Galaxy. I'll work on getting this information added to the wiki.
Victor
On Nov 2, 2010, at 1:10 PM, David Hoover wrote:
I modified universe_wsgi.ini and the files in ~/tool-data/shared/ucsc, then restarted galaxy, but it still downloads data from UCSC instead of the local mirror. Is there something I missed?
David
On Nov 2, 2010, at 1:31 PM, Victor Ruotti wrote:
Hi David, For the table browser we set up here. [galaxy:tool_runners] biomart = local:/// encode_db1 = local:/// hbvar = local:/// microbial_import1 = local:/// ucsc_table_direct1 = http://localgenome.cgi-bin/hgTables
This is not what this section is used for, in fact. The [galaxy:tool_runners] section of the config is used by the job dispatcher to determine whether the tool should run locally or on a cluster (and with what cluster parameters). Thanks, --nate
ucsc_table_direct_archaea1 = local:/// ucsc_table_direct_test1 = local:/// upload1 = local:///
For displaying the actual genome with bed files we changed the file. /galaxy-central/tool-data/shared/ucsc
So it points to our local genome browser.
Hope this helps. Victor
On Nov 2, 2010, at 12:23 PM, David Hoover wrote:
Is there any way of having Galaxy use a local mirror of the UCSC Genome Browser instead of the main site? Is there a central config file somewhere that I can just change genome.ucsc.edu to something else?
David Hoover Helix Systems Staff http://helix.nih.gov _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Right, and a few other things. I had to change the name and id of the tool in the new ucsc_tablebrowser.xml file, and keep the id the same for the param.toold_id.value as well. The new id was added to the list of [galaxy:tool_runners] with local:/// as well. A little roundabout, but doable. Thanks for your help. David On Nov 2, 2010, at 2:35 PM, Nate Coraor wrote: Victor Ruotti wrote:
Hi David, This might help you. http://bitbucket.org/galaxy/galaxy-central/wiki/UCSC2Galaxy
Sorry, this information is a bit outdated. There is a more recent page that covers writing display applications, but it's written from the perspective of adding entirely new display applications rather than linking to an existing browser: http://bitbucket.org/galaxy/galaxy-central/wiki/ExternalDisplayApplications/... The relevant information is that that the site should be given a name and added to: galaxy_dist/tool-data/shared/ucsc/ucsc_build_sites.txt Once done, that name should be added to the parameter 'ucsc_display_sites' in universe_wsgi.ini. This will enable your browser for the "display at ..." links under compatible file types of data in your history. To add your local mirror as a data source tool, you'll need to make a copy of: galaxy_dist/data_source/ucsc_tablebrowser.xml And change the URL in the <inputs> tag to point to your local browser. Once this is done, add the path to your new XML file to 'tool_conf.xml' and restart Galaxy. I'll work on getting this information added to the wiki.
Victor
On Nov 2, 2010, at 1:10 PM, David Hoover wrote:
I modified universe_wsgi.ini and the files in ~/tool-data/shared/ucsc, then restarted galaxy, but it still downloads data from UCSC instead of the local mirror. Is there something I missed?
David
On Nov 2, 2010, at 1:31 PM, Victor Ruotti wrote:
Hi David, For the table browser we set up here. [galaxy:tool_runners] biomart = local:/// encode_db1 = local:/// hbvar = local:/// microbial_import1 = local:/// ucsc_table_direct1 = http://localgenome.cgi-bin/hgTables
This is not what this section is used for, in fact. The [galaxy:tool_runners] section of the config is used by the job dispatcher to determine whether the tool should run locally or on a cluster (and with what cluster parameters). Thanks, --nate
ucsc_table_direct_archaea1 = local:/// ucsc_table_direct_test1 = local:/// upload1 = local:///
For displaying the actual genome with bed files we changed the file. /galaxy-central/tool-data/shared/ucsc
So it points to our local genome browser.
Hope this helps. Victor
On Nov 2, 2010, at 12:23 PM, David Hoover wrote:
Is there any way of having Galaxy use a local mirror of the UCSC Genome Browser instead of the main site? Is there a central config file somewhere that I can just change genome.ucsc.edu to something else?
David Hoover Helix Systems Staff http://helix.nih.gov _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
David Hoover wrote:
Right, and a few other things. I had to change the name and id of the tool in the new ucsc_tablebrowser.xml file, and keep the id the same for the param.toold_id.value as well. The new id was added to the list of [galaxy:tool_runners] with local:/// as well.
Ah yes, a few more steps than I had. I'll get this all into the wiki. The data source tools can run on the cluster if your cluster nodes are able to initiate connections out to their sources (so NAT is okay). The upload tool can also run on the cluster, you just have to set $TEMP to somewhere in a filesystem shared between the Galaxy server and the cluster (e.g. galaxy_dist/database/tmp/) in the environment in which Galaxy is started. --nate
A little roundabout, but doable. Thanks for your help.
David
On Nov 2, 2010, at 2:35 PM, Nate Coraor wrote:
Victor Ruotti wrote:
Hi David, This might help you. http://bitbucket.org/galaxy/galaxy-central/wiki/UCSC2Galaxy
Sorry, this information is a bit outdated. There is a more recent page that covers writing display applications, but it's written from the perspective of adding entirely new display applications rather than linking to an existing browser:
http://bitbucket.org/galaxy/galaxy-central/wiki/ExternalDisplayApplications/...
The relevant information is that that the site should be given a name and added to:
galaxy_dist/tool-data/shared/ucsc/ucsc_build_sites.txt
Once done, that name should be added to the parameter 'ucsc_display_sites' in universe_wsgi.ini. This will enable your browser for the "display at ..." links under compatible file types of data in your history.
To add your local mirror as a data source tool, you'll need to make a copy of:
galaxy_dist/data_source/ucsc_tablebrowser.xml
And change the URL in the <inputs> tag to point to your local browser. Once this is done, add the path to your new XML file to 'tool_conf.xml' and restart Galaxy.
I'll work on getting this information added to the wiki.
Victor
On Nov 2, 2010, at 1:10 PM, David Hoover wrote:
I modified universe_wsgi.ini and the files in ~/tool-data/shared/ucsc, then restarted galaxy, but it still downloads data from UCSC instead of the local mirror. Is there something I missed?
David
On Nov 2, 2010, at 1:31 PM, Victor Ruotti wrote:
Hi David, For the table browser we set up here. [galaxy:tool_runners] biomart = local:/// encode_db1 = local:/// hbvar = local:/// microbial_import1 = local:/// ucsc_table_direct1 = http://localgenome.cgi-bin/hgTables
This is not what this section is used for, in fact. The [galaxy:tool_runners] section of the config is used by the job dispatcher to determine whether the tool should run locally or on a cluster (and with what cluster parameters).
Thanks, --nate
ucsc_table_direct_archaea1 = local:/// ucsc_table_direct_test1 = local:/// upload1 = local:///
For displaying the actual genome with bed files we changed the file. /galaxy-central/tool-data/shared/ucsc
So it points to our local genome browser.
Hope this helps. Victor
On Nov 2, 2010, at 12:23 PM, David Hoover wrote:
Is there any way of having Galaxy use a local mirror of the UCSC Genome Browser instead of the main site? Is there a central config file somewhere that I can just change genome.ucsc.edu to something else?
David Hoover Helix Systems Staff http://helix.nih.gov _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
One other little nugget. If Galaxy is externally authenticated, I can't display custom tracks on my local mirror. It timed out when I tried to display them on the main UCSC site. I guess this is because the bed files are behind the authentication, right? Maybe I should rethink this external authentication... On Nov 2, 2010, at 3:09 PM, Nate Coraor wrote: David Hoover wrote:
Right, and a few other things. I had to change the name and id of the tool in the new ucsc_tablebrowser.xml file, and keep the id the same for the param.toold_id.value as well. The new id was added to the list of [galaxy:tool_runners] with local:/// as well.
Ah yes, a few more steps than I had. I'll get this all into the wiki. The data source tools can run on the cluster if your cluster nodes are able to initiate connections out to their sources (so NAT is okay). The upload tool can also run on the cluster, you just have to set $TEMP to somewhere in a filesystem shared between the Galaxy server and the cluster (e.g. galaxy_dist/database/tmp/) in the environment in which Galaxy is started. --nate
A little roundabout, but doable. Thanks for your help.
David
On Nov 2, 2010, at 2:35 PM, Nate Coraor wrote:
Victor Ruotti wrote:
Hi David, This might help you. http://bitbucket.org/galaxy/galaxy-central/wiki/UCSC2Galaxy
Sorry, this information is a bit outdated. There is a more recent page that covers writing display applications, but it's written from the perspective of adding entirely new display applications rather than linking to an existing browser:
http://bitbucket.org/galaxy/galaxy-central/wiki/ExternalDisplayApplications/...
The relevant information is that that the site should be given a name and added to:
galaxy_dist/tool-data/shared/ucsc/ucsc_build_sites.txt
Once done, that name should be added to the parameter 'ucsc_display_sites' in universe_wsgi.ini. This will enable your browser for the "display at ..." links under compatible file types of data in your history.
To add your local mirror as a data source tool, you'll need to make a copy of:
galaxy_dist/data_source/ucsc_tablebrowser.xml
And change the URL in the <inputs> tag to point to your local browser. Once this is done, add the path to your new XML file to 'tool_conf.xml' and restart Galaxy.
I'll work on getting this information added to the wiki.
Victor
On Nov 2, 2010, at 1:10 PM, David Hoover wrote:
I modified universe_wsgi.ini and the files in ~/tool-data/shared/ucsc, then restarted galaxy, but it still downloads data from UCSC instead of the local mirror. Is there something I missed?
David
On Nov 2, 2010, at 1:31 PM, Victor Ruotti wrote:
Hi David, For the table browser we set up here. [galaxy:tool_runners] biomart = local:/// encode_db1 = local:/// hbvar = local:/// microbial_import1 = local:/// ucsc_table_direct1 = http://localgenome.cgi-bin/hgTables
This is not what this section is used for, in fact. The [galaxy:tool_runners] section of the config is used by the job dispatcher to determine whether the tool should run locally or on a cluster (and with what cluster parameters).
Thanks, --nate
ucsc_table_direct_archaea1 = local:/// ucsc_table_direct_test1 = local:/// upload1 = local:///
For displaying the actual genome with bed files we changed the file. /galaxy-central/tool-data/shared/ucsc
So it points to our local genome browser.
Hope this helps. Victor
On Nov 2, 2010, at 12:23 PM, David Hoover wrote:
Is there any way of having Galaxy use a local mirror of the UCSC Genome Browser instead of the main site? Is there a central config file somewhere that I can just change genome.ucsc.edu to something else?
David Hoover Helix Systems Staff http://helix.nih.gov _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
David Hoover wrote:
One other little nugget. If Galaxy is externally authenticated, I can't display custom tracks on my local mirror. It timed out when I tried to display them on the main UCSC site. I guess this is because the bed files are behind the authentication, right? Maybe I should rethink this external authentication...
It's possible to work around it if you're willing to give up a bit of security. See the "Display at UCSC" section of ApacheProxy: http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy You'll have to add your own mirror to remoteuser.py as well (this list of servers should not be hardcoded but we haven't gotten to fixing that yet). --nate
On Nov 2, 2010, at 3:09 PM, Nate Coraor wrote:
David Hoover wrote:
Right, and a few other things. I had to change the name and id of the tool in the new ucsc_tablebrowser.xml file, and keep the id the same for the param.toold_id.value as well. The new id was added to the list of [galaxy:tool_runners] with local:/// as well.
Ah yes, a few more steps than I had. I'll get this all into the wiki.
The data source tools can run on the cluster if your cluster nodes are able to initiate connections out to their sources (so NAT is okay).
The upload tool can also run on the cluster, you just have to set $TEMP to somewhere in a filesystem shared between the Galaxy server and the cluster (e.g. galaxy_dist/database/tmp/) in the environment in which Galaxy is started.
--nate
A little roundabout, but doable. Thanks for your help.
David
On Nov 2, 2010, at 2:35 PM, Nate Coraor wrote:
Victor Ruotti wrote:
Hi David, This might help you. http://bitbucket.org/galaxy/galaxy-central/wiki/UCSC2Galaxy
Sorry, this information is a bit outdated. There is a more recent page that covers writing display applications, but it's written from the perspective of adding entirely new display applications rather than linking to an existing browser:
http://bitbucket.org/galaxy/galaxy-central/wiki/ExternalDisplayApplications/...
The relevant information is that that the site should be given a name and added to:
galaxy_dist/tool-data/shared/ucsc/ucsc_build_sites.txt
Once done, that name should be added to the parameter 'ucsc_display_sites' in universe_wsgi.ini. This will enable your browser for the "display at ..." links under compatible file types of data in your history.
To add your local mirror as a data source tool, you'll need to make a copy of:
galaxy_dist/data_source/ucsc_tablebrowser.xml
And change the URL in the <inputs> tag to point to your local browser. Once this is done, add the path to your new XML file to 'tool_conf.xml' and restart Galaxy.
I'll work on getting this information added to the wiki.
Victor
On Nov 2, 2010, at 1:10 PM, David Hoover wrote:
I modified universe_wsgi.ini and the files in ~/tool-data/shared/ucsc, then restarted galaxy, but it still downloads data from UCSC instead of the local mirror. Is there something I missed?
David
On Nov 2, 2010, at 1:31 PM, Victor Ruotti wrote:
Hi David, For the table browser we set up here. [galaxy:tool_runners] biomart = local:/// encode_db1 = local:/// hbvar = local:/// microbial_import1 = local:/// ucsc_table_direct1 = http://localgenome.cgi-bin/hgTables
This is not what this section is used for, in fact. The [galaxy:tool_runners] section of the config is used by the job dispatcher to determine whether the tool should run locally or on a cluster (and with what cluster parameters).
Thanks, --nate
ucsc_table_direct_archaea1 = local:/// ucsc_table_direct_test1 = local:/// upload1 = local:///
For displaying the actual genome with bed files we changed the file. /galaxy-central/tool-data/shared/ucsc
So it points to our local genome browser.
Hope this helps. Victor
On Nov 2, 2010, at 12:23 PM, David Hoover wrote:
Is there any way of having Galaxy use a local mirror of the UCSC Genome Browser instead of the main site? Is there a central config file somewhere that I can just change genome.ucsc.edu to something else?
David Hoover Helix Systems Staff http://helix.nih.gov _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Nope, the instructions at the wiki didn't work. Even with changes to remoteuser.py and universe_wsgi.ini, it still times out for UCSC and gives a 401 error for the local site. David On Nov 2, 2010, at 3:26 PM, Nate Coraor wrote: David Hoover wrote:
One other little nugget. If Galaxy is externally authenticated, I can't display custom tracks on my local mirror. It timed out when I tried to display them on the main UCSC site. I guess this is because the bed files are behind the authentication, right? Maybe I should rethink this external authentication...
It's possible to work around it if you're willing to give up a bit of security. See the "Display at UCSC" section of ApacheProxy: http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy You'll have to add your own mirror to remoteuser.py as well (this list of servers should not be hardcoded but we haven't gotten to fixing that yet). --nate
On Nov 2, 2010, at 3:09 PM, Nate Coraor wrote:
David Hoover wrote:
Right, and a few other things. I had to change the name and id of the tool in the new ucsc_tablebrowser.xml file, and keep the id the same for the param.toold_id.value as well. The new id was added to the list of [galaxy:tool_runners] with local:/// as well.
Ah yes, a few more steps than I had. I'll get this all into the wiki.
The data source tools can run on the cluster if your cluster nodes are able to initiate connections out to their sources (so NAT is okay).
The upload tool can also run on the cluster, you just have to set $TEMP to somewhere in a filesystem shared between the Galaxy server and the cluster (e.g. galaxy_dist/database/tmp/) in the environment in which Galaxy is started.
--nate
A little roundabout, but doable. Thanks for your help.
David
On Nov 2, 2010, at 2:35 PM, Nate Coraor wrote:
Victor Ruotti wrote:
Hi David, This might help you. http://bitbucket.org/galaxy/galaxy-central/wiki/UCSC2Galaxy
Sorry, this information is a bit outdated. There is a more recent page that covers writing display applications, but it's written from the perspective of adding entirely new display applications rather than linking to an existing browser:
http://bitbucket.org/galaxy/galaxy-central/wiki/ExternalDisplayApplications/...
The relevant information is that that the site should be given a name and added to:
galaxy_dist/tool-data/shared/ucsc/ucsc_build_sites.txt
Once done, that name should be added to the parameter 'ucsc_display_sites' in universe_wsgi.ini. This will enable your browser for the "display at ..." links under compatible file types of data in your history.
To add your local mirror as a data source tool, you'll need to make a copy of:
galaxy_dist/data_source/ucsc_tablebrowser.xml
And change the URL in the <inputs> tag to point to your local browser. Once this is done, add the path to your new XML file to 'tool_conf.xml' and restart Galaxy.
I'll work on getting this information added to the wiki.
Victor
On Nov 2, 2010, at 1:10 PM, David Hoover wrote:
I modified universe_wsgi.ini and the files in ~/tool-data/shared/ucsc, then restarted galaxy, but it still downloads data from UCSC instead of the local mirror. Is there something I missed?
David
On Nov 2, 2010, at 1:31 PM, Victor Ruotti wrote:
Hi David, For the table browser we set up here. [galaxy:tool_runners] biomart = local:/// encode_db1 = local:/// hbvar = local:/// microbial_import1 = local:/// ucsc_table_direct1 = http://localgenome.cgi-bin/hgTables
This is not what this section is used for, in fact. The [galaxy:tool_runners] section of the config is used by the job dispatcher to determine whether the tool should run locally or on a cluster (and with what cluster parameters).
Thanks, --nate
ucsc_table_direct_archaea1 = local:/// ucsc_table_direct_test1 = local:/// upload1 = local:///
For displaying the actual genome with bed files we changed the file. /galaxy-central/tool-data/shared/ucsc
So it points to our local genome browser.
Hope this helps. Victor
On Nov 2, 2010, at 12:23 PM, David Hoover wrote:
Is there any way of having Galaxy use a local mirror of the UCSC Genome Browser instead of the main site? Is there a central config file somewhere that I can just change genome.ucsc.edu to something else?
David Hoover Helix Systems Staff http://helix.nih.gov _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
OK, finally figured out the problems involved in adding an additional genome browser to the list. 1. The Apache server must be accessible to the Genome Browser hosts. Duh! 2. The correct hostnames need to be added to the following files: ~/lib/galaxy/security/__init__.py ~/lib/galaxy/web/framework/middleware/remoteuser.py 3. A new tablebrowser XML file was created and listed ~/tools/data_source/NIH_ucsc_tablebrowser.xml ~/tool_conf.xml 4. The new ids need to be included in the ucsc_display_sites and [galaxy:tool_runners] section of universe_wsgi.ini. Cheers, David
David Hoover wrote:
OK, finally figured out the problems involved in adding an additional genome browser to the list.
1. The Apache server must be accessible to the Genome Browser hosts. Duh! 2. The correct hostnames need to be added to the following files:
~/lib/galaxy/security/__init__.py ~/lib/galaxy/web/framework/middleware/remoteuser.py
3. A new tablebrowser XML file was created and listed
~/tools/data_source/NIH_ucsc_tablebrowser.xml ~/tool_conf.xml
4. The new ids need to be included in the ucsc_display_sites and [galaxy:tool_runners] section of universe_wsgi.ini.
Cheers, David
Thanks for sending this David. I'll make sure our documentation is updated with all of this information. --nate
participants (3)
-
David Hoover -
Nate Coraor -
Victor Ruotti