1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/41f1db323099/ changeset: r5320:41f1db323099 user: jgoecks date: 2011-04-01 17:36:55 summary: Do not use from_work_dir in Tophat because it causes set_metadata to fail on BAM output when run on a cluster. affected #: 2 files (382 bytes)

--- a/tools/ngs_rna/tophat_wrapper.py Thu Mar 31 19:01:12 2011 -0400 +++ b/tools/ngs_rna/tophat_wrapper.py Fri Apr 01 11:36:55 2011 -0400 @@ -208,6 +208,10 @@ tmp_stderr.close() 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:

--- a/tools/ngs_rna/tophat_wrapper.xml Thu Mar 31 19:01:12 2011 -0400 +++ b/tools/ngs_rna/tophat_wrapper.xml Fri Apr 01 11:36:55 2011 -0400 @@ -397,8 +397,8 @@ ) </filter></data> - <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions" from_work_dir="tophat_out/junctions.bed"/> - <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits" from_work_dir="tophat_out/accepted_hits.bam"/> + <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions"/> + <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits"/></outputs><tests>

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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