Hello all,
I am having some trouble getting a "display at" link to my local UCSC Genome Browser mirror to show up under my Galaxy jobs for viewing, although I can get the link to the online UCSC GB to display. I followed the suggestions in the following thread but it has yielded no results yet: http://gmod.827538.n3.nabble.com/using-local-Genome-Browser-mirror-td1829290... .
Here's what I have tried: - I edited the [galaxy-dir]/tool-data/shared/ucsc/ucsc_build_sites.txt file and duplicated the 'main' UCSC entry but changed the new entry's name to 'internalgb' and changed the URL to point to our local GB with * cgi-bin/hgTracks?* at the end - I set "*ucsc_display_sites = internalgb*" in universe_wsgi.ini - I made a modified copy of [galaxy-dir]/tools/data_source/ucsc_tablebrowser.xml (named HAIB_ucsc_tablebrowser.xml) in the same directory as the other XML files and created a tool link on the left side of the Galaxy page for it by adding it to the tool_conf.xml file (which works fine: when I click on it it loads our local Genome Browser inside the central Galaxy window frame) - I edited the HAIB_ucsc_tablebrowser.xml file according to the recommendation in the thread above: "*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*." So I gave it a unique id (changed ucsc_table_direct1 to HAIB_table_direct1) but kept the tool_id value field the same as the original/main UCSC tablebrowser (ucsc_table_direct1). Then I put the new HAIB id for our local tablebrowser into universe_wsgi.ini under the tool runners section as "*HAIB_table_direct1 = local:///*" - And of course I have restarted Galaxy after each change.
Still after all of this I cannot see a "display at" link for bam & other files from Galaxy for my local UCSC GB. When I change universe_wsgi.ini to have "ucsc_display_sites = internalgb,main" set (for both browsers) the online/main GB will have a "display at" link on Galaxy jobs but no link shows for my local browser mirror. I'm also a little fuzzy on the relation between the ucsc_build_sites.txt file and the "*_ucsc_tablebrowser.xml" files (if any). Any tips as to what I might be missing here?
Thanks! Josh