Hi Dan,

Good catch sir! Genius! It is working now. The spacing was exactly the same
to the eye in vi for all the entries, but once I did a 'set list' in vi to
display formatting characters I saw that 'main' had the tab ^I characters
but my 'internalgb' entry didn't. This must have happened because I did a
"visual copy" with my cursor. Thank you.

-Josh

On Mon, Feb 27, 2012 at 11:09 AM, Daniel Blankenberg <d...@bx.psu.edu> wrote:

> Hi Josh,
>
> It sounds like you are really close to getting this to work. My first
> guess would be that there is an issue with the modified
> ucsc_build_sites.txt file. Can you check that the line you copied is tab
> delimited and not space delimited?
>
>
> Thanks for using Galaxy,
>
> Dan
>
> On Feb 27, 2012, at 11:46 AM, Josh Nielsen wrote:
>
> 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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