2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7627567df99c/ changeset: 7627567df99c user: jgoecks date: 2013-02-04 16:04:41 summary: Use from_work_dir for all Tophat2 output datasets rather than copying datasets in tool wrapper. affected #: 2 files diff -r cef2e9ff0960bab52fd481ec77585b6ecca8dfce -r 7627567df99c879146560ed523f903ed17d12fd6 tools/ngs_rna/tophat2_wrapper.py --- a/tools/ngs_rna/tophat2_wrapper.py +++ b/tools/ngs_rna/tophat2_wrapper.py @@ -260,11 +260,6 @@ if returncode != 0: raise Exception, stderr - # Copy output files from tmp directory to specified files. - shutil.copyfile( os.path.join( "tophat_out", "junctions.bed" ), options.junctions_output_file ) - shutil.copyfile( os.path.join( "tophat_out", "accepted_hits.bam" ), options.accepted_hits_output_file ) - - # TODO: look for errors in program output. except Exception, e: stop_err( 'Error in tophat:\n' + str( e ) ) diff -r cef2e9ff0960bab52fd481ec77585b6ecca8dfce -r 7627567df99c879146560ed523f903ed17d12fd6 tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -356,7 +356,7 @@ </conditional></actions></data> - <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions"> + <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions" from_work_dir="tophat_out/junctions.bed"><actions><conditional name="refGenomeSource.genomeSource"><when value="indexed"> @@ -375,7 +375,7 @@ </conditional></actions></data> - <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits"> + <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits" from_work_dir="tophat_out/accepted_hits.bam"><actions><conditional name="refGenomeSource.genomeSource"><when value="indexed"> https://bitbucket.org/galaxy/galaxy-central/commits/3de3a5a2d9b1/ changeset: 3de3a5a2d9b1 user: jgoecks date: 2013-02-04 16:06:13 summary: Use conditional so that from_work_dir is only active if file exists. This prevents spurious error messages when a tool fails. affected #: 1 file diff -r 7627567df99c879146560ed523f903ed17d12fd6 -r 3de3a5a2d9b1f467ad5a7d855de84b2e2e7888a8 lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -34,11 +34,12 @@ if job_wrapper.dependency_shell_commands: commands = "; ".join( job_wrapper.dependency_shell_commands + [ commands ] ) - # -- Append commands to copy job outputs based on from_work_dir attribute. -- + # Append commands to copy job outputs based on from_work_dir attribute. if include_work_dir_outputs: work_dir_outputs = self.get_work_dir_outputs( job_wrapper ) if work_dir_outputs: - commands += "; " + "; ".join( [ "cp %s %s" % ( source_file, destination ) for ( source_file, destination ) in work_dir_outputs ] ) + commands += "; " + "; ".join( [ "if [ -f %s ] ; then cp %s %s ; fi" % + ( source_file, source_file, destination ) for ( source_file, destination ) in work_dir_outputs ] ) # Append metadata setting commands, we don't want to overwrite metadata # that was copied over in init_meta(), as per established behavior Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.