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.html
.

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
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