Mercurial > repos > jeremie > breakdancer_test

changeset 22:b4f641515363 draft

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Uploaded
author jeremie
date Tue, 01 Jul 2014 10:14:06 -0400
parents 199c0c7d3093
children 298a0a61a20d
files breakdancer.py
diffstat 1 files changed, 1 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/breakdancer.py	Tue Jul 01 10:09:33 2014 -0400
+++ b/breakdancer.py	Tue Jul 01 10:14:06 2014 -0400
@@ -5,7 +5,6 @@
 
 parser = argparse.ArgumentParser(description='')
 
-parser.add_argument('-x', dest='binPath')
 parser.add_argument ( '-i1', dest='input_bam', help='the bam input file' )
 parser.add_argument ( '-o1', dest='output_raw', help='the output file' )
 parser.add_argument ( '-o2', dest='output_vcf', help='the output file' )
@@ -16,7 +15,7 @@
 
 currentDir = os.path.dirname(os.path.abspath(__file__))
 
-binPath = args.binPath
+binPath = os.environ['BREAKDANCER_BIN']
 bam2cfg = binPath+"/bam2cfg.pl"
 breakdancer = binPath+"/breakdancer-max"
 breakdancer2vcf = binPath+"/breakdancer2vcf.py"