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comparison strelka_wrapper.py @ 9:0e8e6011082b

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Strelka Workflow 0.0.2
author mini
date Fri, 26 Sep 2014 15:51:35 +0200
parents 2cee4ed50058
children 137e05f24336
comparison
equal deleted inserted replaced
8:2cee4ed50058 9:0e8e6011082b
96 root_dir= args.scriptPath 96 root_dir= args.scriptPath
97 expected_dir="for_tests" 97 expected_dir="for_tests"
98 job_dir=os.getcwd() 98 job_dir=os.getcwd()
99 analysis_dir=job_dir + "/StrelkaAnalysis" 99 analysis_dir=job_dir + "/StrelkaAnalysis"
100 config_script=root_dir + "/configureStrelkaWorkflow.pl" 100 config_script=root_dir + "/configureStrelkaWorkflow.pl"
101 tmp_dir = "tmp" #tempfile.mkdtemp( prefix='tmp-strelkaAnalysis-' ) 101 tmp_dir = tempfile.mkdtemp( prefix='tmp-strelkaAnalysis-' )
102 config_ini = "%s/config.ini" % (tmp_dir) 102 config_ini = "%s/config.ini" % (tmp_dir)
103 103
104 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) 104 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)
105 105
106 106
111 if os.path.exists(analysis_dir): 111 if os.path.exists(analysis_dir):
112 sys.exit("'" + analysis_dir + "' already exist, if you are executing this tool from galaxy it should not happen") 112 sys.exit("'" + analysis_dir + "' already exist, if you are executing this tool from galaxy it should not happen")
113 113
114 114
115 # creating index if needed 115 # creating index if needed
116 os.environ['PATH']= root_dir + "/opt/samtools:" + os.environ['PATH'] 116 #os.environ['PATH']= root_dir + "/opt/samtools:" + os.environ['PATH']
117 bam_filenames = [ args.tumorBam, args.normalBam ] 117 bam_filenames = [ args.tumorBam, args.normalBam ]
118 index_bam_files( bam_filenames, tmp_dir ) 118 index_bam_files( bam_filenames, tmp_dir )
119 fasta_files = [ args.refFile ] 119 fasta_files = [ args.refFile ]
120 index_fasta_files( fasta_files, tmp_dir ) 120 index_fasta_files( fasta_files, tmp_dir )
121 121
127 my_Popen(cmdbash, "copy_default_file_err", tmp_dir, "Error during the copy of default config file, maybe it was removed") 127 my_Popen(cmdbash, "copy_default_file_err", tmp_dir, "Error during the copy of default config file, maybe it was removed")
128 else: 128 else:
129 if not os.path.exists(args.configFile): 129 if not os.path.exists(args.configFile):
130 print( "The path to your configuration File seems to be wrong, use another one or custom option", file=sys.stderr) 130 print( "The path to your configuration File seems to be wrong, use another one or custom option", file=sys.stderr)
131 cmdbash="cp %s %s" % (args.configFile, config_ini) 131 cmdbash="cp %s %s" % (args.configFile, config_ini)
132 my_Popen(cmdbash, "copy_default_file_err", tmp_dir, "Error during the copy of default config file, maybe it was removed") 132 my_Popen(cmdbash, "copy_default_file_err", tmp_dir, "Error during the copy of the selected config file")
133 133
134 134
135 135
136 136
137 #configuration of workflow 137 #configuration of workflow