Mercurial > repos > mini > strelka
diff strelka_wrapper.py @ 14:ca84a74ff567
corriging bug in environment variable
author | mini |
---|---|
date | Wed, 01 Oct 2014 12:21:13 +0200 |
parents | 137e05f24336 |
children | 8260a4188b08 |
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--- 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__()