Mercurial > repos > sanbi-uwc > data_manager_rnastar_index_builder

comparison data_manager/rnastar_index_builder.py @ 13:e905fcc6fd15 draft

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planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 4c88ff739e2fb47369e5256151eb55cc5cb47c9d
author sanbi-uwc
date Tue, 16 Feb 2016 02:11:37 -0500
parents a42dbab7917c
children 70316134a316
comparison
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12:a42dbab7917c 13:e905fcc6fd15
34 if 'GALAXY_SLOTS' in environ: 34 if 'GALAXY_SLOTS' in environ:
35 nslots = environ['GALAXY_SLOTS'] 35 nslots = environ['GALAXY_SLOTS']
36 else: 36 else:
37 nslots = 1 37 nslots = 1
38 38
39 cmdline_str = 'STAR --runMode genomeGenerate --genomeDir {} --genomeFastaFiles {} --runThreadsN {}'.format( 39 cmdline_str = 'STAR --runMode genomeGenerate --genomeDir {} --genomeFastaFiles {} --runThreadN {}'.format(
40 output_directory, 40 output_directory,
41 fasta_filename, 41 fasta_filename,
42 nslots) 42 nslots)
43 cmdline = shlex.split(cmdline_str) 43 cmdline = shlex.split(cmdline_str)
44 # cmdline = ('touch', '{}/foo'.format(output_directory)) 44 #cmdline = ('touch', '{}/foo'.format(output_directory))
45 try: 45 try:
46 check_call(cmdline) 46 check_call(cmdline)
47 except CalledProcessError: 47 except CalledProcessError:
48 print("Error building RNA STAR index", file=sys.stderr) 48 print("Error building RNA STAR index", file=sys.stderr)
49 return (output_directory) 49 return (output_directory)