details: http://www.bx.psu.edu/hg/galaxy/rev/c92bca0f3fc4 changeset: 2765:c92bca0f3fc4 user: Kelly Vincent kpvincent@bx.psu.edu date: Thu Sep 24 14:09:17 2009 -0400 description: Modified solid to fastq converter tool to specify path to perl script that does conversion
1 file(s) affected in this change:
tools/next_gen_conversion/solid_to_fastq.py
diffs (21 lines):
diff -r 0baf06b86ca0 -r c92bca0f3fc4 tools/next_gen_conversion/solid_to_fastq.py --- a/tools/next_gen_conversion/solid_to_fastq.py Thu Sep 24 13:54:12 2009 -0400 +++ b/tools/next_gen_conversion/solid_to_fastq.py Thu Sep 24 14:09:17 2009 -0400 @@ -30,7 +30,7 @@ tmpf = tempfile.NamedTemporaryFile() #forward reads if options.input3 != "None" and options.input4 != "None": tmpr = tempfile.NamedTemporaryFile() #reverse reads - cmd1 = "bwa_solid2fastq_modified.pl 'yes' %s %s %s %s %s %s %s 2>&1" %(tmpf.name,tmpr.name,None,options.input1,options.input2,options.input3,options.input4) + cmd1 = "%s/bwa_solid2fastq_modified.pl 'yes' %s %s %s %s %s %s %s 2>&1" %(os.path.split(sys.argv[0])[0], tmpf.name,tmpr.name,None,options.input1,options.input2,options.input3,options.input4) try: os.system(cmd1) os.system('gunzip -c %s >> %s' %(tmpf.name,options.output1)) @@ -40,7 +40,7 @@ tmpr.close() # if single-end data else: - cmd1 = "bwa_solid2fastq_modified.pl 'no' %s %s %s %s %s %s %s 2>&1" % (tmpf.name, None, None, options.input1, options.input2, None, None) + cmd1 = "%s/bwa_solid2fastq_modified.pl 'no' %s %s %s %s %s %s %s 2>&1" % (os.path.split(sys.argv[0])[0], tmpf.name, None, None, options.input1, options.input2, None, None) try: os.system(cmd1) os.system('gunzip -c %s >> %s' % (tmpf.name, options.output1))