I have been trying to send data to our Gbrowse2 servers from within
I found some information from Greg Von Kuster (below) explaining how
to change the configuration settings.
I edited ~/universe_wsgi.ini and ~/tool-data/shared/gbrowse/
We have python 2.6 and the file ~/lib/galaxy/datatypes/interval.py has
the following in the class Gff section:
self.add_display_app( 'gbrowse', 'display in Gbrowse',
'as_gbrowse_display_file', 'gbrowse_links' )
but I still only see "display at UCSC" - there is no "display at
Is there another file I need to edit in order to get this link to show
as an option?
MRC Molecular Haematology Unit
> > On Mon, Mar 15, 2010 at 10:46 AM, Jelle Scholtalbers <
> > j.scholtalbers at gmail.com> wrote:
> >> 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
> >> 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
> >> generated from for example the
> >> ~/tool-data/shared/gbrowse/gbrowse_build_sites.txt
> >> Cheers,
> >> Jelle
> >> On Fri, Mar 12, 2010 at 3:25 PM, Greg Von Kuster <greg at
> bx.psu.edu> wrote:
> >>> This requires only configuration settings, not an actual tool
> >>> 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
> >>> 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/
> >>> test http://dev.wormbase.org/db/seq/gbrowse/c_elegans/
> >>> 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.