Mercurial > repos > sanbi-uwc > data_manager_rnastar_index_builder

comparison data_manager/rnastar_index_builder.py @ 14:70316134a316 draft default tip

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planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit fbb3a55395065d6ea8ed23189fa65813b93d52a3
author sanbi-uwc
date Wed, 09 Mar 2016 05:45:58 -0500
parents e905fcc6fd15
children
comparison
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13:e905fcc6fd15 14:70316134a316
39 cmdline_str = 'STAR --runMode genomeGenerate --genomeDir {} --genomeFastaFiles {} --runThreadN {}'.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))
45 try: 44 try:
46 check_call(cmdline) 45 check_call(cmdline)
47 except CalledProcessError: 46 except CalledProcessError:
48 print("Error building RNA STAR index", file=sys.stderr) 47 print("Error building RNA STAR index", file=sys.stderr)
49 return (output_directory) 48 return (output_directory)