Hello Rochak,
For wormbase:
1 ) Have this in your universe_wsgi.ini file:
# Comma separated list of UCSC / gbrowse browsers to use for viewing
ucsc_display_sites = main,test,archaea
gbrowse_display_sites = wormbase
2) Have something like this in your gbrowse_build_sites.txt file (
white space is a <tab> char, and c_elegans is a comma-separated
list of genome builds ):
#Harvested from http://www.wormbase.org/db/seq/gbrowse/wormbase/
wormbase http://dev.wormbase.org/db/seq/gbrowse/c_elegans/
c_elegans,<other builds>
That should be all that is needed to display the following in your
history item:
3: Wormbase on I:12740595..12780384
97 lines, format: gff3, database: c_elegans
Info: Wormbase on I:12740595..12780384
Greg Von Kuster
Galaxy Development Team
Rochak Neupane wrote:
When a data is in BED format or Customtrack and build is
on of ucsc, a link shows up with a link to "display at UCSC main".
I was wondering if this would be possible to do with gbrowse for data
in Gff or Gff3.
I added gbrowse links to:
tool-data/shared/gbrowse/gbrowse_build_sites.txt
for data in gff format, lib/galaxy/datatypes/interval.py has
add_display_app in it, but I was not able to get a link on my dataset.
What exactly do I have to do to get a link to "display in Gbrowse"?
thanks!
rochak
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