# HG changeset patch
# User jeremie
# Date 1404224046 14400
# Node ID b4f641515363d0d6f63a53dd527c89d0d0be5eaf
# Parent  199c0c7d3093f7203489f4e0b9e23f0fb6624d6f
Uploaded

diff -r 199c0c7d3093 -r b4f641515363 breakdancer.py
--- 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"