Mercurial > repos > sanbi-uwc > data_manager_novocraft_index_builder

comparison data_manager/novocraft_index_builder.py @ 11:a9b725202132 draft

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planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 9ea1c9c5fdf0ed65170469f809b81ba9e82f91d3
author sanbi-uwc
date Mon, 07 Mar 2016 02:27:51 -0500
parents 68b7023c6a2f
children 283eec05d1de
comparison
equal deleted inserted replaced
10:68b7023c6a2f 11:a9b725202132
35 print("Output directory path already exists but is not a directory: {}".format(target_directory), 35 print("Output directory path already exists but is not a directory: {}".format(target_directory),
36 file=sys.stderr) 36 file=sys.stderr)
37 elif not os.path.exists(target_directory): 37 elif not os.path.exists(target_directory):
38 os.mkdir(target_directory) 38 os.mkdir(target_directory)
39 39
40 if 'GALAXY_SLOTS' in os.environ: 40 index_filename = os.path.join(target_directory,"%.nix" % sequence_id)
41 nslots = os.environ['GALAXY_SLOTS'] 41 cmdline_str = 'novoindex {} {}'.format(index_filename, fasta_filename)
42 else: 42 cmdline = shlex.split(cmdline_str)
43 nslots = 1
44 43
45 #cmdline_str = 'STAR --runMode genomeGenerate --genomeDir {} --genomeFastaFiles {} --runThreadN {}'.format( 44 #index_filename = 'foo'
46 # target_directory, 45 #cmdline = ('touch', '{}/{}'.format(target_directory, index_filename))
47 # fasta_filename,
48 # nslots)
49 #cmdline = shlex.split(cmdline_str)
50 index_filename = 'foo'
51 cmdline = ('touch', '{}/{}'.format(target_directory, index_filename))
52 try: 46 try:
53 check_call(cmdline) 47 check_call(cmdline)
54 except CalledProcessError: 48 except CalledProcessError:
55 print("Error building RNA STAR index", file=sys.stderr) 49 print("Error building RNA STAR index", file=sys.stderr)
56 50
57 data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=os.path.join(target_directory, index_filename) ) 51 data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=index_filename )
58 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) 52 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
59 return ( index_filename )
60 53
61 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ): 54 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
62 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) 55 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
63 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] ) 56 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
64 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry ) 57 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )