Sending Data To Gbrowse

8.7 years ago by

Penn State University

This requires only configuration settings, not an actual tool like Epigraph. Displaying in GBrowse is done the same way as displaying in UCSC. In you universe_wsgi.ini file, look for hte following setting, and set your GBrowse accordingly - you may only want 1 site instead of the 3 in the sample. # Comma separated list of bx / UCSC / gbrowse / GeneTrack browsers to use for viewing bx_display_sites = main ucsc_display_sites = main,test,archaea,ucla gbrowse_display_sites = main,test,tair Next, make the setting in ~/tool- data/shared/gbrowse/gbrowse_build_sites.txt - here are the sample settings ( note that each corresponds to what you configured in your universe_wsgi.ini file ). White spaces are tabs in this file, and the first value in each line ( e.g., main, test ) is the link label that points to the GBrowse site whose URL is in the 2nd column. The 3rd column of each line is the valid builds for which the link will be displayed ( see below ). Note that the sample builds are no longer valid, they should be value slike ce2, ce3, etc - see ~/tool- data/shared/ucsc/builds.txt for valid values ). # wormbase sites / supported genomes main http://www.wormbase.org/db/seq/gbgff/c_elegans/ c_elegans,c_br iggsae,c_remanei,c_brenneri,c_japonica,p_pristionchus,b_malayi test http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ c_eleg ans,c_briggsae,c_remanei,c_brenneri,c_japonica,p_pristionchus,b_malayi tair http://arabidopsis.org/cgi-bin/gbrowse/ arabidopsis_tair8,arabidopsis When you have the correct configuration settings, you'll see a link in history items ( here is an example - display in Wormbase main ) whose genome build matches one of the configured builds. Greg Von Kuster Galaxy Development Team greg@bx.psu.edu

ADD COMMENT • link written 8.7 years ago by Greg Von Kuster ♦ 810

Hi Greg, thank you for the explanation, could this also be included somewhere in the wiki? Although I do get far I don't get the tracks to display in my GBrowse. The link does redirect me to the appropriate gbrowse that I specified, the uploaded track is displayed as: "could not fetch data for http://galaxyserver/galaxy/root/display_as?id=4047&display_app=c_elega ns&authz_method=display_at" with the label "galaxyserver/display_as". When I then follow that link I actually see the data as GFF, but it seems GBrowse can't retrieve it somehow. This was tested under: Galaxy-central - 3528:48e83411aa91 and GBrowse 1.995 Two other things: - under python 2.6 the links appear, under 2.4 they don't. - The links are displayed as "display in wormbase" and the display_app="c_elegans". This seems to be harcoded at galaxy.datatypes.interval line 572, would be nice to have that dynamically generated from for example the ~/tool-data/shared/gbrowse/gbrowse_build_sites.txt Cheers, Jelle

ADD REPLY • link written 8.7 years ago by Jelle Scholtalbers • 360

Hi Greg, I just figured it might have something to do with the proxy.. And indeed removing the proxy/adding exception did work (...), the track is displayed as expected. However this only works for the test case where Galaxy is not behind a LDAP auth. When it is behind LDAP, access is probably denied. I will see what I can do about this, but at least the basis is working :) Cheers, Jelle On Mon, Mar 15, 2010 at 10:46 AM, Jelle Scholtalbers <

ADD REPLY • link written 8.7 years ago by Jelle Scholtalbers • 360

What I now did to circumvent the issue with ldap, is to have this little piece in my httpd.conf: <location galaxy="" root="" display_as=""> SetEnv AUTHENTICATE_SAMACCOUNTNAME galaxy Satisfy Any </location> RequestHeader set REMOTE_USER %{AUTHENTICATE_sAMAccountName}e There is probably a better way, but this does the job for now. Cheers, Jelle On Mon, Mar 15, 2010 at 11:42 AM, Jelle Scholtalbers <

ADD REPLY • link written 8.7 years ago by Jelle Scholtalbers • 360

Hi, I am trying to view my galaxy datasets in our local GBrowse install. I have set the parameters in both the universe_wsgi file and ~/tool-data/shared/gbrowse/gbrowse_build_sites.txt as outlined below. I have added a GBrowse option called "local" and included the relevant builds, however I cannot get the link to display in appropriate datasets. Are there any further configuration steps I need to follow? Thanks Shaun Webb Quoting Greg Von Kuster <greg@bx.psu.edu>: -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

ADD REPLY • link written 8.6 years ago by SHAUN WEBB • 70

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