--- a/strelka_wrapper.py	Fri Sep 26 14:33:07 2014 +0200
+++ b/strelka_wrapper.py	Fri Sep 26 15:51:35 2014 +0200
@@ -98,7 +98,7 @@
     job_dir=os.getcwd()
     analysis_dir=job_dir + "/StrelkaAnalysis"
     config_script=root_dir + "/configureStrelkaWorkflow.pl"
-    tmp_dir = "tmp"  #tempfile.mkdtemp( prefix='tmp-strelkaAnalysis-' )
+    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)
@@ -113,7 +113,7 @@
     
 
     # creating index if needed
-    os.environ['PATH']= root_dir + "/opt/samtools:" + os.environ['PATH']
+    #os.environ['PATH']= root_dir + "/opt/samtools:" + os.environ['PATH']
     bam_filenames = [ args.tumorBam, args.normalBam ]
     index_bam_files( bam_filenames, tmp_dir )
     fasta_files = [ args.refFile ]
@@ -129,7 +129,7 @@
     	if not os.path.exists(args.configFile):
 	     print( "The path to your configuration File seems to be wrong, use another one or custom option", file=sys.stderr)
     	cmdbash="cp %s %s" % (args.configFile, config_ini)
-        my_Popen(cmdbash, "copy_default_file_err", tmp_dir, "Error during the copy of default config file, maybe it was removed")
+        my_Popen(cmdbash, "copy_default_file_err", tmp_dir, "Error during the copy of the selected config file")