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Make SAM_to_BAM tool write temporary files to job working directory rather than generic temp space.

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Jeremy Goecks
2013-07-02 09:25:55 -04:00
parent 828c4953f5
commit 8a461dfac2
1 changed files with 1 additions and 1 deletions
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tools/samtools/sam_to_bam.py
+1 -1
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@@ -42,7 +42,7 @@ def __main__():
except:
sys.stdout.write( 'Could not determine Samtools version\n' )
tmp_dir = tempfile.mkdtemp()
tmp_dir = tempfile.mkdtemp( dir='.' )
if not options.ref_file or options.ref_file == 'None':
# We're using locally cached reference sequences( e.g., /galaxy/data/equCab2/sam_index/equCab2.fa ).
# The indexes for /galaxy/data/equCab2/sam_index/equCab2.fa will be contained in