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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