1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/babda116a4c0/
changeset: babda116a4c0
user: natefoo
date: 2012-04-02 21:38:02
summary: I missed a call to a renamed method in the job manager.
affected #: 1 file
diff -r 07eb5affb4c0c74f1bf95d2fb850f926d4defaf2 -r babda116a4c0193c2ee4941d09ac78940098fece lib/galaxy/jobs/manager.py
--- a/lib/galaxy/jobs/manager.py
+++ b/lib/galaxy/jobs/manager.py
@@ -89,7 +89,7 @@
log.warning( "(%s) Tool '%s' removed from tool config, unable to recover job" % ( job.id, job.tool_id ) )
JobWrapper( job, self ).fail( 'This tool was disabled before the job completed. Please contact your Galaxy administrator.' )
else:
- job.handler = self.__select_handler( job ) # handler's recovery method will take it from here
+ job.handler = self.__get_handler( job ) # handler's recovery method will take it from here
log.info( "(%d) Job in '%s' state had no handler at job manager startup, assigned '%s' handler" % ( job.id, job.state, job.handler ) )
if self.sa_session.dirty:
self.sa_session.flush()
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/e8e6bb539b85/
changeset: e8e6bb539b85
user: dan
date: 2012-04-02 17:00:56
summary: Fix for DiskObjectStore._construct_path recieving extra keywords.
affected #: 1 file
diff -r 6ceefdcedee595904231c4bc2ee78417bfec637a -r e8e6bb539b85533d8aff54adbacfcfd548ba8a8e lib/galaxy/objectstore/__init__.py
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -223,7 +223,7 @@
if not os.path.exists(path):
return self._construct_path(obj, base_dir=base_dir, dir_only=dir_only, extra_dir=extra_dir, extra_dir_at_root=extra_dir_at_root, alt_name=alt_name)
- def _construct_path(self, obj, old_style=False, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+ def _construct_path(self, obj, old_style=False, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, **kwargs):
""" Construct the expected absolute path for accessing the object
identified by `obj`.id.
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/6ceefdcedee5/
changeset: 6ceefdcedee5
user: dan
date: 2012-04-02 16:48:27
summary: Fix for call to object_store.update_from_file for collect primary data in tools/__init__.py.
affected #: 1 file
diff -r 24b474fd29bcfddabd996e985c72872e21c8c0f8 -r 6ceefdcedee595904231c4bc2ee78417bfec637a lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2180,7 +2180,7 @@
sa_session=self.sa_session )
self.app.security_agent.copy_dataset_permissions( outdata.dataset, child_dataset.dataset )
# Move data from temp location to dataset location
- self.app.object_store.update_from_file(child_dataset.dataset, filename, create=True)
+ self.app.object_store.update_from_file(child_dataset.dataset, file_name=filename, create=True)
self.sa_session.add( child_dataset )
self.sa_session.flush()
child_dataset.set_size()
@@ -2247,7 +2247,7 @@
self.sa_session.add( primary_data )
self.sa_session.flush()
# Move data from temp location to dataset location
- self.app.object_store.update_from_file(primary_data.dataset, filename, create=True)
+ self.app.object_store.update_from_file(primary_data.dataset, file_name=filename, create=True)
primary_data.set_size()
primary_data.name = "%s (%s)" % ( outdata.name, designation )
primary_data.info = outdata.info
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/24b474fd29bc/
changeset: 24b474fd29bc
user: dan
date: 2012-04-02 16:09:00
summary: Fix for --multiallelic in Unified Genotyper.
affected #: 1 file
diff -r 4dd7564268fcd4f5bd3275fa3b5da012b7adefb5 -r 24b474fd29bcfddabd996e985c72872e21c8c0f8 tools/gatk/unified_genotyper.xml
--- a/tools/gatk/unified_genotyper.xml
+++ b/tools/gatk/unified_genotyper.xml
@@ -138,6 +138,7 @@
--excludeAnnotation "${annotation}"
#end for
#end if
+ ${analysis_param_type.multiallelic}
'
## #if str( $analysis_param_type.snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff':
## -p '--annotation "SnpEff"'
@@ -145,7 +146,6 @@
## #else:
## -p '--excludeAnnotation "SnpEff"'
## #end if
- ${analysis_param_type.multiallelic}
#end if
</command><inputs>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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