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Sorry, this information is a bit outdated.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
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