1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/07f3f601d645/
changeset: 07f3f601d645
user: dan
date: 2011-10-28 17:38:55
summary: Fix for refresh on change in workflow run interface triggering actual running of workflow.
affected #: 1 file
diff -r 9a6e51c4efeb1b901cb4cc5b2c494577b5f11ad8 -r 07f3f601d645f07b76b196879ecd6d1c68c5b5d4 lib/galaxy/web/controllers/workflow.py
--- a/lib/galaxy/web/controllers/workflow.py
+++ b/lib/galaxy/web/controllers/workflow.py
@@ -1480,10 +1480,10 @@
trans.sa_session.add( workflow_invocation )
invocations.append({'outputs': outputs,
'new_history': new_history})
- trans.sa_session.flush()
- return trans.fill_template( "workflow/run_complete.mako",
- workflow=stored,
- invocations=invocations )
+ trans.sa_session.flush()
+ return trans.fill_template( "workflow/run_complete.mako",
+ workflow=stored,
+ invocations=invocations )
else:
# Prepare each step
missing_tools = []
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/786a5d6c56c7/
changeset: 786a5d6c56c7
user: greg
date: 2011-10-27 19:52:05
summary: Eliminate forgotten (and not wanted) PostJobAction code when generating a workflow it's dict representation for rendering as an svg image in the tool shed.
affected #: 1 file
diff -r 753196399060239c365040aa6ecb18cba345b69e -r 786a5d6c56c77b592598df8e32b227cb6e5cb63f lib/galaxy/webapps/community/controllers/workflow.py
--- a/lib/galaxy/webapps/community/controllers/workflow.py
+++ b/lib/galaxy/webapps/community/controllers/workflow.py
@@ -339,12 +339,6 @@
workflow.has_errors = True
# Stick this in the step temporarily.
step.temp_input_connections = step_dict[ 'input_connections' ]
- # Unpack and add post-job actions.
- post_job_actions = step_dict.get( 'post_job_actions', {} )
- for name, pja_dict in post_job_actions.items():
- pja = PostJobAction( pja_dict[ 'action_type' ],
- step, pja_dict[ 'output_name' ],
- pja_dict[ 'action_arguments' ] )
steps.append( step )
steps_by_external_id[ step_dict[ 'id' ] ] = step
# Second pass to deal with connections between steps.
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/753196399060/
changeset: 753196399060
user: greg
date: 2011-10-27 19:37:48
summary: Fix for rendering workflow metadata.
affected #: 1 file
diff -r c528fab7ea8c89ab55cb9977d5916c72e5170546 -r 753196399060239c365040aa6ecb18cba345b69e templates/webapps/community/repository/common.mako
--- a/templates/webapps/community/repository/common.mako
+++ b/templates/webapps/community/repository/common.mako
@@ -168,7 +168,11 @@
%for workflow_dict in workflow_dicts:
<%
workflow_name = workflow_dict[ 'name' ]
- steps = workflow_dict[ 'steps' ]
+ if 'steps' in workflow_dict:
+ ## Initially steps were not stored in the metadata record.
+ steps = workflow_dict[ 'steps' ]
+ else:
+ steps = []
format_version = workflow_dict[ 'format-version' ]
annotation = workflow_dict[ 'annotation' ]
%>
@@ -178,7 +182,6 @@
</td><td>
%if 'steps' in workflow_dict:
- ## Initially steps were not stored in the metadata record.
${len( steps )}
%else:
unknown
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/216d4f094804/
changeset: 216d4f094804
user: dan
date: 2011-10-27 16:54:42
summary: Have Picard MergeSamFiles use return code to determine tool error.
affected #: 1 file
diff -r 0ba260ea43c4e9613965e9f32705a118bab7c3ec -r 216d4f09480468bb01ee56df9a393c5b740fe51d tools/samtools/sam_merge.xml
--- a/tools/samtools/sam_merge.xml
+++ b/tools/samtools/sam_merge.xml
@@ -9,6 +9,7 @@
I=${i.input}
#end for
2> $outlog
+ || echo "Error running Picard MergeSamFiles" >&2
</command><inputs><param name="title" label="Name for the output merged bam file" type="text" default="Merged.bam"
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/37fb9b1fb62d/
changeset: 37fb9b1fb62d
user: dan
date: 2011-10-26 22:03:47
summary: Allow Picard based Merge BAM Files tool to work on sam inputs as well as the previously accepted bam.
affected #: 1 file
diff -r f335b8bbb91f575f1ffac466c53b907e8623a9a8 -r 37fb9b1fb62de6a304c6c500d9610b7eea2cf2aa tools/samtools/sam_merge.xml
--- a/tools/samtools/sam_merge.xml
+++ b/tools/samtools/sam_merge.xml
@@ -16,10 +16,10 @@
<param name="mergeSD" value="true" type="boolean" label="Merge all component bam file headers into the merged bam file"
truevalue="true" falsevalue="false" checked="yes"
help="Control the MERGE_SEQUENCE_DICTIONARIES flag for Picard MergeSamFiles. Default (true) correctly propagates read groups and other important metadata" />
- <param name="input1" label="First file" type="data" format="bam" />
- <param name="input2" label="with file" type="data" format="bam" help="Need to add more files? Use controls below." />
+ <param name="input1" label="First file" type="data" format="bam,sam" />
+ <param name="input2" label="with file" type="data" format="bam,sam" help="Need to add more files? Use controls below." /><repeat name="inputs" title="Input Files">
- <param name="input" label="Add file" type="data" format="bam" />
+ <param name="input" label="Add file" type="data" format="bam,sam" /></repeat></inputs><outputs>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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