Hi Josh,

Correct, to get the display functionality to work, your first two steps are 
sufficient.  The other steps are only needed if you want to allow users to use 
your local mirror as a data source inside of Galaxy. If you don't want users to 
be able to use your local mirror as a data source, which may have faster 
loading times or additional data loaded that does not exist in UCSC's public 
site, you can safely remove the entry from your tool_conf.xml file without 
affecting the ability for your users to send files for display.


Thanks for using Galaxy,

Dan


On Feb 27, 2012, at 1:13 PM, Josh Nielsen wrote:

> One more thing while I'm at it. For clarification would only the first two 
> steps I listed be sufficient to get the "display at" link in Galaxy? If so 
> what is the benefit of the other steps (other than having an actual link to 
> your local genome browser mirror in Galaxy)? There's nothing that ties my 
> internalgb entry to the new tool_id I created is there?
> 
> 
> On Mon, Feb 27, 2012 at 11:58 AM, Josh Nielsen <jniel...@hudsonalpha.com> 
> wrote:
> 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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> 

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