details:
http://www.bx.psu.edu/hg/galaxy/rev/c8bf73ed4594
changeset: 1743:c8bf73ed4594
user: Greg Von Kuster <greg(a)bx.psu.edu>
date: Thu Mar 26 09:34:05 2009 -0400
description:
i18n fix: dataset.info should not be translated since it will generally not have an entry
in the catalog. Wormbase fixes: URL to main site corrected, and all supported builds
added to gbrowse_build_sites.txt.
4 file(s) affected in this change:
templates/root/history_common.mako
tool-data/shared/gbrowse/gbrowse_build_sites.txt
tools/data_source/wormbase.xml
universe_wsgi.ini.sample
diffs (58 lines):
diff -r 02843f56b812 -r c8bf73ed4594 templates/root/history_common.mako
--- a/templates/root/history_common.mako Wed Mar 25 11:51:30 2009 -0400
+++ b/templates/root/history_common.mako Thu Mar 26 09:34:05 2009 -0400
@@ -51,7 +51,7 @@
The job creating this dataset was cancelled before completion.
</div>
%elif data_state == "empty":
- <div>${_('No data:
')}<i>${_(data.display_info())}</i></div>
+ <div>${_('No data:
')}<i>${data.display_info()}</i></div>
%elif data_state == "ok":
<div>
${data.blurb},
@@ -63,7 +63,7 @@
<span
class="${data.dbkey}">${_(data.dbkey)}</span>
%endif
</div>
- <div class="info">${_('Info:
')}${_(data.display_info())} </div>
+ <div class="info">${_('Info:
')}${data.display_info()}</div>
<div>
%if data.has_data:
<a href="${h.url_for( action='display',
id=data.id, tofile='yes', toext=data.ext )}"
target="_blank">save</a>
diff -r 02843f56b812 -r c8bf73ed4594 tool-data/shared/gbrowse/gbrowse_build_sites.txt
--- a/tool-data/shared/gbrowse/gbrowse_build_sites.txt Wed Mar 25 11:51:30 2009 -0400
+++ b/tool-data/shared/gbrowse/gbrowse_build_sites.txt Thu Mar 26 09:34:05 2009 -0400
@@ -1,5 +1,3 @@
-#Harvested from
http://www.wormbase.org/db/seq/gbrowse/wormbase/
-#wormbase
http://gvk.bx.psu.edu/cgi-bin/gbrowse/volvox? briggsae,briggsae_cb25,brugia,elegans,elegans_gmap,elegans_pmap,fly,fly31,nGASP,nGASP_submissions,remanei,wormbase,ws77,yeast_chr1
-#Harvested from
http://flybase.bio.indiana.edu/cgi-bin/gbrowse/dmel/
-#flybase
http://flybase.bio.indiana.edu/cgi-bin/gbrowse/dmel/ dana,dere,dgri,dmel,dmoj,dper,dpse,dsec,dsim,dvir,dwil,dyak,dmelstocks
-elegans
http://brie3.cshl.edu:9000/db/seq/gbrowse/elegans/ cb1,cb2,cb3,ce1,ce2,ce3,ce4
\ No newline at end of file
+# 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
+test
http://dev.wormbase.org/db/seq/gbrowse/c_elegans/
c_elegans,c_briggsae,c_remanei,c_brenneri,c_japonica,p_pristionchus,b_malayi
diff -r 02843f56b812 -r c8bf73ed4594 tools/data_source/wormbase.xml
--- a/tools/data_source/wormbase.xml Wed Mar 25 11:51:30 2009 -0400
+++ b/tools/data_source/wormbase.xml Thu Mar 26 09:34:05 2009 -0400
@@ -2,7 +2,7 @@
<tool name="Wormbase" id="wormbase"
tool_type="data_source" URL_method="post">
<description>server</description>
<command interpreter="python">data_source.py $output</command>
- <inputs
action="http://www.wormbase.org/db/seq/gbrowse/c_elegans/"
check_values="false" target="_top">
+ <inputs
action="http://www.wormbase.org/db/seq/gbgff/c_elegans/"
check_values="false" target="_top">
<display>go to Wormbase server $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl"
value="/tool_runner?tool_id=wormbase" />
</inputs>
diff -r 02843f56b812 -r c8bf73ed4594 universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample Wed Mar 25 11:51:30 2009 -0400
+++ b/universe_wsgi.ini.sample Thu Mar 26 09:34:05 2009 -0400
@@ -115,7 +115,7 @@
# Comma separated list of UCSC / gbrowse browsers to use for viewing
ucsc_display_sites = main,test,archaea
-gbrowse_display_sites =
c_elegans,c_briggsae,c_remanei,c_brenneri,c_japonica,p_pristionchus,b_malayi
+gbrowse_display_sites = main,test
# Serving static files (needed if running standalone)
static_enabled = True