Mercurial > repos > mini > strelka
diff strelka_wrapper.py @ 9:0e8e6011082b
Strelka Workflow 0.0.2
author | mini |
---|---|
date | Fri, 26 Sep 2014 15:51:35 +0200 |
parents | 2cee4ed50058 |
children | 137e05f24336 |
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--- a/strelka_wrapper.py Fri Sep 26 14:33:07 2014 +0200 +++ b/strelka_wrapper.py Fri Sep 26 15:51:35 2014 +0200 @@ -98,7 +98,7 @@ job_dir=os.getcwd() analysis_dir=job_dir + "/StrelkaAnalysis" config_script=root_dir + "/configureStrelkaWorkflow.pl" - tmp_dir = "tmp" #tempfile.mkdtemp( prefix='tmp-strelkaAnalysis-' ) + 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) @@ -113,7 +113,7 @@ # creating index if needed - os.environ['PATH']= root_dir + "/opt/samtools:" + os.environ['PATH'] + #os.environ['PATH']= root_dir + "/opt/samtools:" + os.environ['PATH'] bam_filenames = [ args.tumorBam, args.normalBam ] index_bam_files( bam_filenames, tmp_dir ) fasta_files = [ args.refFile ] @@ -129,7 +129,7 @@ if not os.path.exists(args.configFile): print( "The path to your configuration File seems to be wrong, use another one or custom option", file=sys.stderr) cmdbash="cp %s %s" % (args.configFile, config_ini) - my_Popen(cmdbash, "copy_default_file_err", tmp_dir, "Error during the copy of default config file, maybe it was removed") + my_Popen(cmdbash, "copy_default_file_err", tmp_dir, "Error during the copy of the selected config file")