Mercurial > repos > mini > strelka
comparison strelka_wrapper.py @ 17:8260a4188b08
solved conf_file.ini pb
| author | mini |
|---|---|
| date | Wed, 01 Oct 2014 13:45:33 +0200 |
| parents | ca84a74ff567 |
| children | 3c10d88b55ad |
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| 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__() |