1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/e4d1dd3bdd0d/
changeset: e4d1dd3bdd0d
user: natefoo
date: 2012-02-06 19:03:24
summary: Set a descriptive job name when using the DRMAA runner
affected #: 1 file
diff -r 73e2dd2c815bf289751951d6127be2a14d7163e6 -r e4d1dd3bdd0dfbe8562ac352d08b1f9b497d7063 lib/galaxy/jobs/runners/drmaa.py
--- a/lib/galaxy/jobs/runners/drmaa.py
+++ b/lib/galaxy/jobs/runners/drmaa.py
@@ -170,6 +170,7 @@
efile = "%s.drmerr" % os.path.join(job_wrapper.working_directory, job_wrapper.get_id_tag())
jt = self.ds.createJobTemplate()
jt.remoteCommand = "%s/galaxy_%s.sh" % (self.app.config.cluster_files_directory, job_wrapper.get_id_tag())
+ jt.jobName = "g%s_%s_%s" % ( job_wrapper.job_id, job_wrapper.tool.id, job_wrapper.user.replace( '@', '__at__' ) )
jt.outputPath = ":%s" % ofile
jt.errorPath = ":%s" % efile
native_spec = self.get_native_spec( runner_url )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/e38a9eb21336/
changeset: e38a9eb21336
user: greg
date: 2012-02-06 16:19:43
summary: Load empty tool sections into the in-memory tool_panel dictionary, just don't display them in the tool panel. Also include a fix for reactivating or unintallting a tool shed repository that includes tools - ToolVersion ovjects cannot be marked deleted.
affected #: 3 files
diff -r 281bd9a8feddf90af8edf13acfa752809f7824d5 -r e38a9eb21336ce56ba6c5ec53e7492853c2c4088 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -295,7 +295,7 @@
self.load_workflow_tag_set( sub_elem, elems )
elif sub_elem.tag == 'label':
self.load_label_tag_set( sub_elem, elems )
- if key not in panel_dict and section.elems:
+ if key not in panel_dict:
panel_dict[ key ] = section
def load_tool( self, config_file, guid=None ):
"""
diff -r 281bd9a8feddf90af8edf13acfa752809f7824d5 -r e38a9eb21336ce56ba6c5ec53e7492853c2c4088 lib/galaxy/web/controllers/admin_toolshed.py
--- a/lib/galaxy/web/controllers/admin_toolshed.py
+++ b/lib/galaxy/web/controllers/admin_toolshed.py
@@ -499,18 +499,9 @@
metadata = repository.metadata
repository_tools_tups = get_repository_tools_tups( trans.app, metadata )
guids_to_activate = [ repository_tool_tup[1] for repository_tool_tup in repository_tools_tups ]
- # Undelete the tool_version for each guid.
+ # Make sure we have a tool_version for each guid.
for guid_to_activate in guids_to_activate:
- tool_version = get_tool_version( trans.app, guid_to_activate )
- if tool_version:
- if tool_version.deleted:
- # This should not happen as we are currently not marking tool versions as deleted
- # upon deactivation. We may decide to eliminate the tool_version.deleted column
- # at some point, but we'll keep it for now in case we decide its useful.
- tool_version.deleted = False
- trans.sa_session.add( tool_version )
- trans.sa_session.flush()
- else:
+ if not get_tool_version( trans.app, guid_to_activate ):
# We're somehow missing a tool_version, so create a new one.
tool_version = trans.model.ToolVersion( tool_id=guid_to_activate, tool_shed_repository=repository )
trans.sa_session.add( tool_version )
diff -r 281bd9a8feddf90af8edf13acfa752809f7824d5 -r e38a9eb21336ce56ba6c5ec53e7492853c2c4088 templates/root/tool_menu.mako
--- a/templates/root/tool_menu.mako
+++ b/templates/root/tool_menu.mako
@@ -365,22 +365,25 @@
${render_workflow( key, val, False )}
%elif key.startswith( 'section' ):
<% section = val %>
- <div class="toolSectionTitle" id="title_${section.id}">
- <span>${section.name}</span>
- </div>
- <div id="${section.id}" class="toolSectionBody">
- <div class="toolSectionBg">
- %for section_key, section_val in section.elems.items():
- %if section_key.startswith( 'tool' ):
- ${render_tool( section_val, True )}
- %elif section_key.startswith( 'workflow' ):
- ${render_workflow( section_key, section_val, True )}
- %elif section_key.startswith( 'label' ):
- ${render_label( section_val )}
- %endif
- %endfor
+ ## Render the section only if it is not empty.
+ %if section.elems:
+ <div class="toolSectionTitle" id="title_${section.id}">
+ <span>${section.name}</span></div>
- </div>
+ <div id="${section.id}" class="toolSectionBody">
+ <div class="toolSectionBg">
+ %for section_key, section_val in section.elems.items():
+ %if section_key.startswith( 'tool' ):
+ ${render_tool( section_val, True )}
+ %elif section_key.startswith( 'workflow' ):
+ ${render_workflow( section_key, section_val, True )}
+ %elif section_key.startswith( 'label' ):
+ ${render_label( section_val )}
+ %endif
+ %endfor
+ </div>
+ </div>
+ %endif
%elif key.startswith( 'label' ):
${render_label( val )}
%endif
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/32d1ab3262ea/
changeset: 32d1ab3262ea
user: jgoecks
date: 2012-02-05 18:53:23
summary: Handle instance where BAMDataProvider iterator is None; this can occur when trying to fetch additional data.
affected #: 1 file
diff -r 84baec18959cb7f48f450f9aa676aaa1882044c1 -r 32d1ab3262ea4d45e1cae1f43f44e43d3c8899d8 lib/galaxy/visualization/tracks/data_providers.py
--- a/lib/galaxy/visualization/tracks/data_providers.py
+++ b/lib/galaxy/visualization/tracks/data_providers.py
@@ -646,6 +646,10 @@
max_high - highest coordinate for the returned reads
message - error/informative message
"""
+ # No iterator indicates no reads.
+ if iterator is None:
+ return { 'data': [], 'message': None }
+
# Decode strand from read flag.
def decode_strand( read_flag, mask ):
strand_flag = ( read_flag & mask == 0 )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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