Hi all,
Is it possible to customize Galaxy to use a mirror of the genome browser?
Thanks,
Keith Lamont
Keith,
For getting data, the easiest thing to do is to create a new tool config. Copy "tools/data_source/ucsc_tablebrowser.xml" in your Galaxy instance to something like "tools/data_source/ ucsc_tablebrowser_local_mirror.xml". Then in that file change (1) the name and id attributes of the <tool> element to something unique and (2) the action attribute of the <inputs> element to point to the URL of your mirror. Then add the new tool config to your "tool_conf.xml".
As long as your UCSC mirror is a reasonably recent version, it will then communicate properly with your local Galaxy instance.
Please let us know if you have any problems.
Thanks, James
On Apr 4, 2008, at 3:38 PM, Keith Lamont wrote:
Hi all,
Is it possible to customize Galaxy to use a mirror of the genome browser?
Thanks,
Keith Lamont
galaxy-user mailing list galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
Keith,
Also, if you are interested in being able to display datasets in your local browser mirror, you can modify the file "static/ucsc/ ucsc_build_sites.txt". You will need a line like:
site_name http://URL build1,build2,build3...
The third field is the list of builds supported by that site, you can likely just copy the line for "main", or modify the list if you have a partial mirror.
You will also need to add "site_name" to "ucsc_display_sites" in universe_wsgi.ini
Thanks, James
On Apr 4, 2008, at 3:38 PM, Keith Lamont wrote:
Hi all,
Is it possible to customize Galaxy to use a mirror of the genome browser?
Thanks,
Keith Lamont
galaxy-user mailing list galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
galaxy-user@lists.galaxyproject.org
-
James Taylor -
Keith Lamont