1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/e34f80fe39ec/
changeset: e34f80fe39ec
user: dan
date: 2012-04-24 19:56:42
summary: Add rerun and show info buttons to discarded datasets.
affected #: 1 file
diff -r 17d02d9fa4dd3aae05fa5a9a5a74dac099b2b03e -r e34f80fe39ecab5d76cd20ded0eeac449351b482 templates/root/history_common.mako
--- a/templates/root/history_common.mako
+++ b/templates/root/history_common.mako
@@ -172,6 +172,12 @@
<div>
The job creating this dataset was cancelled before completion.
</div>
+ <div>
+ <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information tooltip"></a>
+ %if for_editing:
+ <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle tooltip"></a>
+ %endif
+ </div>
%elif data_state == 'setting_metadata':
<div>${_('Metadata is being Auto-Detected.')}</div>
%elif data_state == "empty":
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/ce32134aec56/
changeset: ce32134aec56
user: dannon
date: 2012-04-24 17:53:35
summary: Workflow editor fix for the case where RenameActions had null action arguments vs being unspecified or {} as expected. This situation exists in very few rename actions and hasn't been reproduced, may be legacy workflow steps.
affected #: 1 file
diff -r ea722ae95cb7c99742c081bcd17bddc441dfa2fb -r ce32134aec5687e9ee5386a7742ab97b950f2a5e lib/galaxy/jobs/actions/post.py
--- a/lib/galaxy/jobs/actions/post.py
+++ b/lib/galaxy/jobs/actions/post.py
@@ -203,11 +203,10 @@
@classmethod
def get_config_form(cls, trans):
form = """
- if ((pja.action_arguments !== undefined) && (pja.action_arguments.newname !== undefined)){
+ if (pja.action_arguments && pja.action_arguments.newname){
p_str += "<label for='pja__"+pja.output_name+"__RenameDatasetAction__newname'>New output name:</label>\
<input type='text' name='pja__"+pja.output_name+"__RenameDatasetAction__newname' value=\\"" + pja.action_arguments.newname.replace(/"/g, """) + "\\"/>";
}
-
else{
p_str += "<label for='pja__"+pja.output_name+"__RenameDatasetAction__newname'>New output name:</label>\
<input type='text' name='pja__"+pja.output_name+"__RenameDatasetAction__newname' value=''/>";
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/ea722ae95cb7/
changeset: ea722ae95cb7
user: jgoecks
date: 2012-04-24 17:05:47
summary: Minor curation of data providers: (a) rename gff data provider to match similar providers and (b) add note about how to extend GTF tabix to support GFF/GFF3 as well.
affected #: 2 files
diff -r 562a4f68a4f848bb4be992b27b67fff01ad652c8 -r ea722ae95cb7c99742c081bcd17bddc441dfa2fb lib/galaxy/visualization/tracks/data_providers.py
--- a/lib/galaxy/visualization/tracks/data_providers.py
+++ b/lib/galaxy/visualization/tracks/data_providers.py
@@ -1009,9 +1009,9 @@
return { 'data': results, 'message': message }
-class GFFDataProvider( TracksDataProvider ):
+class RawGFFDataProvider( TracksDataProvider ):
"""
- Provide data from GFF file.
+ Provide data from GFF file that has not been indexed.
NOTE: this data provider does not use indices, and hence will be very slow
for large datasets.
@@ -1059,9 +1059,16 @@
return { 'data': results, 'message': message }
class GtfTabixDataProvider( TabixDataProvider ):
+ """
+ Returns data from GTF datasets that are indexed via tabix.
+ """
def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ):
# Loop through lines and group by transcript_id; each group is a feature.
+
+ # TODO: extend this code or use code in gff_util to process GFF/3 as well
+ # and then create a generic GFFDataProvider that can be used with both
+ # raw and tabix datasets.
features = {}
for count, line in enumerate( iterator ):
line_attrs = parse_gff_attributes( line.split('\t')[8] )
diff -r 562a4f68a4f848bb4be992b27b67fff01ad652c8 -r ea722ae95cb7c99742c081bcd17bddc441dfa2fb lib/galaxy/web/controllers/tracks.py
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -486,7 +486,7 @@
data = None
# TODO: for raw data requests, map dataset type to provider using dict in data_providers.py
if isinstance( dataset.datatype, Gff ):
- data = GFFDataProvider( original_dataset=dataset ).get_data( chrom, low, high, **kwargs )
+ data = RawGFFDataProvider( original_dataset=dataset ).get_data( chrom, low, high, **kwargs )
data[ 'dataset_type' ] = 'interval_index'
data[ 'extra_info' ] = None
elif isinstance( dataset.datatype, Bed ):
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/d01699e14cb0/
changeset: d01699e14cb0
user: greg
date: 2012-04-23 21:59:04
summary: Enhance the "find workflows" feature in the tool shed and installe dtool shed repositories to allow for finding all workflows if the search criteria is blank.
affected #: 2 files
diff -r 98f47fbe0a4f289e7078d5f0aab1c03caeeedf49 -r d01699e14cb0c8edcd4720db2fb6c4b4c284d7e6 lib/galaxy/webapps/community/controllers/repository.py
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -475,13 +475,16 @@
# This can only occur when there is a multi-select grid with check boxes and an operation,
# and the user clicked the operation button without checking any of the check boxes.
return trans.show_error_message( "No items were selected." )
- workflow_names = [ item.lower() for item in util.listify( kwd.get( 'workflow_name', '' ) ) ]
- exact_matches = params.get( 'exact_matches', '' )
- exact_matches_checked = CheckboxField.is_checked( exact_matches )
- match_tuples = []
- ok = True
- if workflow_names:
- ok, match_tuples = self.__search_repository_metadata( trans, exact_matches_checked, workflow_names=workflow_names )
+ if 'find_workflows_button' in kwd:
+ workflow_names = [ item.lower() for item in util.listify( kwd.get( 'workflow_name', '' ) ) ]
+ exact_matches = params.get( 'exact_matches', '' )
+ exact_matches_checked = CheckboxField.is_checked( exact_matches )
+ match_tuples = []
+ ok = True
+ if workflow_names:
+ ok, match_tuples = self.__search_repository_metadata( trans, exact_matches_checked, workflow_names=workflow_names )
+ else:
+ ok, match_tuples = self.__search_repository_metadata( trans, exact_matches_checked, workflow_names=[], all_workflows=True )
if ok:
kwd[ 'match_tuples' ] = match_tuples
# Render the list view
@@ -506,6 +509,9 @@
else:
message = "No search performed - each field must contain the same number of comma-separated items."
status = "error"
+ else:
+ exact_matches_checked = False
+ workflow_names = []
exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked )
return trans.fill_template( '/webapps/community/repository/find_workflows.mako',
webapp=webapp,
@@ -593,7 +599,7 @@
exact_matches_check_box=exact_matches_check_box,
message=message,
status=status )
- def __search_repository_metadata( self, trans, exact_matches_checked, tool_ids='', tool_names='', tool_versions='', workflow_names='' ):
+ def __search_repository_metadata( self, trans, exact_matches_checked, tool_ids='', tool_names='', tool_versions='', workflow_names='', all_workflows=False ):
match_tuples = []
ok = True
for repository_metadata in trans.sa_session.query( model.RepositoryMetadata ):
@@ -661,6 +667,8 @@
for workflow_name in workflow_names:
if self.__in_workflow_dict( workflow_dict, exact_matches_checked, workflow_name ):
match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
+ elif all_workflows and 'workflows' in metadata:
+ match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
return ok, match_tuples
def __in_workflow_dict( self, workflow_dict, exact_matches_checked, workflow_name ):
workflow_dict_workflow_name = workflow_dict[ 'name' ].lower()
diff -r 98f47fbe0a4f289e7078d5f0aab1c03caeeedf49 -r d01699e14cb0c8edcd4720db2fb6c4b4c284d7e6 templates/webapps/community/repository/find_workflows.mako
--- a/templates/webapps/community/repository/find_workflows.mako
+++ b/templates/webapps/community/repository/find_workflows.mako
@@ -26,7 +26,7 @@
<div class="toolFormTitle">Search repositories for workflows</div><div class="toolFormBody"><div class="form-row">
- Enter a workflow name to find repositories that contain workflows matching the search criteria.<br/><br/>
+ Enter a workflow name to find repositories that contain workflows matching the search criteria, or leave blank to find all repositories that contain a workflow.<br/><br/>
Comma-separated strings may be entered to expand search criteria.
</div><div style="clear: both"></div>
@@ -46,7 +46,7 @@
</div><div style="clear: both"></div><div class="form-row">
- <input type="submit" value="Search repositories"/>
+ <input type="submit" name="find_workflows_button" value="Search repositories"/></div></form></div>
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/98f47fbe0a4f/
changeset: 98f47fbe0a4f
user: jgoecks
date: 2012-04-23 21:29:37
summary: Update Trinity wrapper to support most recent versions.
affected #: 1 file
diff -r 6d551feac6c0780979a1ce551a5430990473d864 -r 98f47fbe0a4f289e7078d5f0aab1c03caeeedf49 tools/ngs_rna/trinity_all.xml
--- a/tools/ngs_rna/trinity_all.xml
+++ b/tools/ngs_rna/trinity_all.xml
@@ -1,5 +1,5 @@
<tool id="trinity_all" name="Trinity" version="0.0.1">
- <!-- Run all steps of Trinity-Inchworm, Chrysalis, and Butterfly-in a single step. Wrapper status is alpha. -->
+ <!-- Supports Trinity r2012-04-22-beta and perhaps a few versions earlier. Wrapper is alpha status. --><description>De novo assembly of RNA-Seq data</description><requirements><requirement type="package">trinity</requirement>
@@ -35,8 +35,10 @@
#end if
#end if
+ --kmer_method meryl
+
## CPU and butterfly options.
- --CPU 4 --run_butterfly --bfly_opts "-V 10 --stderr" > $trinity_log 2>&1
+ --CPU 4 --bfly_opts "-V 10 --stderr" > $trinity_log 2>&1
</command><inputs><conditional name="inputs">
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/6d551feac6c0/
changeset: 6d551feac6c0
user: greg
date: 2012-04-23 20:50:27
summary: More fixes for retrieving updates for an installed tool shed repository.
affected #: 1 file
diff -r dd44d4e5219a279400a56825b2ff6e2e81683c98 -r 6d551feac6c0780979a1ce551a5430990473d864 lib/galaxy/webapps/community/controllers/repository.py
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -876,6 +876,7 @@
repository = get_repository_by_name_and_owner( trans, name, owner )
repo_dir = repository.repo_path
repo = hg.repository( get_configured_ui(), repo_dir )
+ latest_ctx = get_changectx_for_changeset( repo, changeset_revision )
from_update_manager = webapp == 'update_manager'
if from_update_manager:
update = 'true'
@@ -889,6 +890,7 @@
# If changeset_revision is the repository tip, we know there are no additional updates for the tools.
if from_update_manager:
return no_update
+ # Return the same value for changeset_revision and latest_changeset_revision.
url += repository.tip
else:
repository_metadata = get_repository_metadata_by_changeset_revision( trans,
@@ -902,9 +904,6 @@
else:
# Return the same value for changeset_revision and latest_changeset_revision.
url += changeset_revision
- # Get the ctx_rev for the changeset_revision.
- latest_ctx = get_changectx_for_changeset( repo, changeset_revision )
- url += '&latest_ctx_rev=%s' % str( latest_ctx.rev() )
else:
# The changeset_revision column in the repository_metadata table has been
# updated with a new changeset_revision value since the repository was cloned.
@@ -965,7 +964,6 @@
url += repository_metadata.changeset_revision
# Get the ctx_rev for the discovered changeset_revision.
latest_ctx = get_changectx_for_changeset( repo, repository_metadata.changeset_revision )
- url += '&latest_ctx_rev=%s' % str( latest_ctx.rev() )
found = True
break
if not found:
@@ -979,6 +977,7 @@
if from_update_manager:
return no_update
url += changeset_revision
+ url += '&latest_ctx_rev=%s' % str( latest_ctx.rev() )
return trans.response.send_redirect( url )
@web.expose
def browse_repositories( self, trans, **kwd ):
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/dd44d4e5219a/
changeset: dd44d4e5219a
user: greg
date: 2012-04-23 20:19:42
summary: Fix for getting updates to an installed tool shed repository where no updates are available.
affected #: 1 file
diff -r 476ce0b78713d5b42ef3e7f6e09b8450496a3692 -r dd44d4e5219a279400a56825b2ff6e2e81683c98 lib/galaxy/webapps/community/controllers/repository.py
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -874,6 +874,8 @@
changeset_revision = params.get( 'changeset_revision', None )
webapp = params.get( 'webapp', 'community' )
repository = get_repository_by_name_and_owner( trans, name, owner )
+ repo_dir = repository.repo_path
+ repo = hg.repository( get_configured_ui(), repo_dir )
from_update_manager = webapp == 'update_manager'
if from_update_manager:
update = 'true'
@@ -884,8 +886,7 @@
url += '&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \
( repository.name, repository.user.username, changeset_revision )
if changeset_revision == repository.tip:
- # If changeset_revision is the repository tip, then
- # we know there are no additional updates for the tools.
+ # If changeset_revision is the repository tip, we know there are no additional updates for the tools.
if from_update_manager:
return no_update
url += repository.tip
@@ -898,12 +899,15 @@
# repository, then we know there are no additional updates for the tools.
if from_update_manager:
return no_update
- url += changeset_revision
+ else:
+ # Return the same value for changeset_revision and latest_changeset_revision.
+ url += changeset_revision
+ # Get the ctx_rev for the changeset_revision.
+ latest_ctx = get_changectx_for_changeset( repo, changeset_revision )
+ url += '&latest_ctx_rev=%s' % str( latest_ctx.rev() )
else:
# The changeset_revision column in the repository_metadata table has been
# updated with a new changeset_revision value since the repository was cloned.
- repo_dir = repository.repo_path
- repo = hg.repository( get_configured_ui(), repo_dir )
# Load each tool in the repository's changeset_revision to generate a list of
# tool guids, since guids differentiate tools by id and version.
ctx = get_changectx_for_changeset( repo, changeset_revision )
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/476ce0b78713/
changeset: 476ce0b78713
user: natefoo
date: 2012-04-23 20:04:45
summary: Fix the tasks runner that I broke when I split job management into multiple processes.
affected #: 1 file
diff -r c8f4f73e9199fc419a221647ccf2337e7e59ed10 -r 476ce0b78713d5b42ef3e7f6e09b8450496a3692 lib/galaxy/jobs/runners/tasks.py
--- a/lib/galaxy/jobs/runners/tasks.py
+++ b/lib/galaxy/jobs/runners/tasks.py
@@ -83,7 +83,7 @@
for task in tasks:
tw = TaskWrapper(task, job_wrapper.queue)
task_wrappers.append(tw)
- self.app.job_manager.dispatcher.put(tw)
+ self.app.job_manager.job_handler.dispatcher.put(tw)
tasks_incomplete = False
count_complete = 0
sleep_time = 1
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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