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comparison strelka_wrapper.py @ 17:8260a4188b08

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solved conf_file.ini pb
author mini
date Wed, 01 Oct 2014 13:45:33 +0200
parents ca84a74ff567
children 3c10d88b55ad
comparison
equal deleted inserted replaced
16:024468e8638c 17:8260a4188b08
56 command = 'samtools faidx %s %s' % ( fasta_filename, fasta_index_filename ) 56 command = 'samtools faidx %s %s' % ( fasta_filename, fasta_index_filename )
57 my_Popen( command, "fasta_index_stderr", tmp_dir, "Error during indexation of fasta file :" + fasta_filename) 57 my_Popen( command, "fasta_index_stderr", tmp_dir, "Error during indexation of fasta file :" + fasta_filename)
58 58
59 def __main__(): 59 def __main__():
60 #Manage options 60 #Manage options
61 print(os.environ['PATH'])
61 parser = argparse.ArgumentParser() 62 parser = argparse.ArgumentParser()
62 parser.add_argument( '-t', '--tumorBam', help='path to tumor bam file', required = False ) 63 parser.add_argument( '-t', '--tumorBam', help='path to tumor bam file', required = False )
63 parser.add_argument( '-n', '--normalBam', help='path to tumor bam file', required = False ) 64 parser.add_argument( '-n', '--normalBam', help='path to tumor bam file', required = False )
64 parser.add_argument( '-r', '--refFile', help='path to tumor bam file', required = False ) 65 parser.add_argument( '-r', '--refFile', help='path to tumor bam file', required = False )
65 parser.add_argument( '-c', '--configFile', help='path to tumor bam file', required = False ) 66 parser.add_argument( '-c', '--configFile', help='path to tumor bam file', required = False )
137 cmd="make -C " + analysis_dir 138 cmd="make -C " + analysis_dir
138 print("**** starting workflow.") 139 print("**** starting workflow.")
139 print("**** workflow cmd: '" + cmd + "'") 140 print("**** workflow cmd: '" + cmd + "'")
140 my_Popen( cmd, "workflow_stderr", tmp_dir, "Error during workflow execution !") 141 my_Popen( cmd, "workflow_stderr", tmp_dir, "Error during workflow execution !")
141 print("**** completed workflow execution") 142 print("**** completed workflow execution")
143
144 cmdbash="cp %s %s" % (config_ini, analysis_dir + "/config.ini")
145 my_Popen(cmdbash, "copy_final_conf_file_err", tmp_dir, "Error during the copy of conf file after job is done, quite strange...")
146
142 147
143 if __name__=='__main__': 148 if __name__=='__main__':
144 __main__() 149 __main__()