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.

templates/root/history_common.mako

@@ -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>

tool-data/shared/gbrowse/gbrowse_build_sites.txt

@@ -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
+# 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

tools/data_source/wormbase.xml

@@ -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>

universe_wsgi.ini.sample

@@ -115,7 +115,7 @@ use_new_layout = true
 
 # 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