Hi,
I have been trying to send data to our Gbrowse2 servers from within Galaxy. 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/ gbrowse_build_sites.txt
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 GBrowse" link
Is there another file I need to edit in order to get this link to show as an option?
Thanks, Nicki
--------------------- Nicki Gray MRC Molecular Haematology Unit 01865 222434
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 http://galaxyserver/galaxy/root/display_as?id=4047&display_app=c_elegans...
"
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
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
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_briggsae,c_remanei,c_brenneri,c_japonica,p_pristionchus,b_malayi
c_elegans ,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.