diff strelka_wrapper.py @ 14:ca84a74ff567

corriging bug in environment variable

--- a/strelka_wrapper.py	Tue Sep 30 11:44:07 2014 +0200
+++ b/strelka_wrapper.py	Wed Oct 01 12:21:13 2014 +0200
@@ -7,7 +7,6 @@
 """
 A wrapper script for running the GenomeAnalysisTK.jar commands.
 """
-
 from __future__ import print_function
 import sys, argparse, os, tempfile, subprocess, shutil
 from binascii import unhexlify
@@ -58,7 +57,6 @@
             my_Popen( command, "fasta_index_stderr", tmp_dir, "Error during indexation of fasta file :" + fasta_filename)
 
 def __main__():
-
     #Manage options
     parser = argparse.ArgumentParser()                                             
     parser.add_argument( '-t', '--tumorBam', help='path to tumor bam file', required = False )
@@ -96,7 +94,7 @@
     tmp_dir = tempfile.mkdtemp( prefix='tmp-strelkaAnalysis-' )
     config_ini = "%s/config.ini" % (tmp_dir)
 
-    #print("root_dir: " + root_dir + "\njob_dir :" + job_dir + "\nanalysis_dir :" + analysis_dir + "\nconfig_script :" + config_script + "\ntmp_dir :" + tmp_dir + "\nconfig_ini :" +  config_ini)
+    print("root_dir: " + root_dir + "\njob_dir :" + job_dir + "\nanalysis_dir :" + analysis_dir + "\nconfig_script :" + config_script + "\ntmp_dir :" + tmp_dir + "\nconfig_ini :" +  config_ini)
 
 
     #verifying eveything's ok
@@ -142,3 +140,5 @@
     my_Popen( cmd, "workflow_stderr", tmp_dir, "Error during workflow execution !")   
     print("**** completed workflow execution")
 
+if __name__=='__main__':
+    __main__()