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comparison strelka_wrapper.py @ 14:ca84a74ff567

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corriging bug in environment variable
author mini
date Wed, 01 Oct 2014 12:21:13 +0200
parents 137e05f24336
children 8260a4188b08
comparison
equal deleted inserted replaced
12:3421b0fbec61 14:ca84a74ff567
5 #For Geviteam 2014 5 #For Geviteam 2014
6 6
7 """ 7 """
8 A wrapper script for running the GenomeAnalysisTK.jar commands. 8 A wrapper script for running the GenomeAnalysisTK.jar commands.
9 """ 9 """
10
11 from __future__ import print_function 10 from __future__ import print_function
12 import sys, argparse, os, tempfile, subprocess, shutil 11 import sys, argparse, os, tempfile, subprocess, shutil
13 from binascii import unhexlify 12 from binascii import unhexlify
14 from string import Template 13 from string import Template
15 from galaxy import eggs 14 from galaxy import eggs
56 #need to index this bam file 55 #need to index this bam file
57 command = 'samtools faidx %s %s' % ( fasta_filename, fasta_index_filename ) 56 command = 'samtools faidx %s %s' % ( fasta_filename, fasta_index_filename )
58 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)
59 58
60 def __main__(): 59 def __main__():
61
62 #Manage options 60 #Manage options
63 parser = argparse.ArgumentParser() 61 parser = argparse.ArgumentParser()
64 parser.add_argument( '-t', '--tumorBam', help='path to tumor bam file', required = False ) 62 parser.add_argument( '-t', '--tumorBam', help='path to tumor bam file', required = False )
65 parser.add_argument( '-n', '--normalBam', help='path to tumor bam file', required = False ) 63 parser.add_argument( '-n', '--normalBam', help='path to tumor bam file', required = False )
66 parser.add_argument( '-r', '--refFile', help='path to tumor bam file', required = False ) 64 parser.add_argument( '-r', '--refFile', help='path to tumor bam file', required = False )
94 analysis_dir=job_dir + "/StrelkaAnalysis" 92 analysis_dir=job_dir + "/StrelkaAnalysis"
95 config_script=root_dir + "/configureStrelkaWorkflow.pl" 93 config_script=root_dir + "/configureStrelkaWorkflow.pl"
96 tmp_dir = tempfile.mkdtemp( prefix='tmp-strelkaAnalysis-' ) 94 tmp_dir = tempfile.mkdtemp( prefix='tmp-strelkaAnalysis-' )
97 config_ini = "%s/config.ini" % (tmp_dir) 95 config_ini = "%s/config.ini" % (tmp_dir)
98 96
99 #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) 97 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)
100 98
101 99
102 #verifying eveything's ok 100 #verifying eveything's ok
103 if not os.path.isfile(config_script): 101 if not os.path.isfile(config_script):
104 sys.exit("ERROR: The strelka workflow must be built prior to running. See installation instructions in '$root_dir/README'") 102 sys.exit("ERROR: The strelka workflow must be built prior to running. See installation instructions in '$root_dir/README'")
140 print("**** starting workflow.") 138 print("**** starting workflow.")
141 print("**** workflow cmd: '" + cmd + "'") 139 print("**** workflow cmd: '" + cmd + "'")
142 my_Popen( cmd, "workflow_stderr", tmp_dir, "Error during workflow execution !") 140 my_Popen( cmd, "workflow_stderr", tmp_dir, "Error during workflow execution !")
143 print("**** completed workflow execution") 141 print("**** completed workflow execution")
144 142
143 if __name__=='__main__':
144 __main__()