# HG changeset patch
# User jeremie
# Date 1404223773 14400
# Node ID 199c0c7d3093f7203489f4e0b9e23f0fb6624d6f
# Parent  b122ca66efc726ba9d8c8b37566f7c1ace5bbd3d
Uploaded

diff -r b122ca66efc7 -r 199c0c7d3093 breakdancer.py
--- a/breakdancer.py	Tue Jul 01 10:09:05 2014 -0400
+++ b/breakdancer.py	Tue Jul 01 10:09:33 2014 -0400
@@ -5,6 +5,7 @@
 
 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' )
@@ -14,10 +15,11 @@
 errorFile = tmp_dir+"/errorLog"
 
 currentDir = os.path.dirname(os.path.abspath(__file__))
-bam2cfg = "./bam2cfg.pl"
-# breakdancer = "/usr/bin/breakdancer-max"
-breakdancer = "breakdancer-max"
-breakdancer2vcf = "./breakdancer2vcf.py"
+
+binPath = args.binPath
+bam2cfg = binPath+"/bam2cfg.pl"
+breakdancer = binPath+"/breakdancer-max"
+breakdancer2vcf = binPath+"/breakdancer2vcf.py"
 
 
 def bam2cfg(args):