Mercurial > repos > sanbi-uwc > data_manager_novocraft_index_builder
changeset 11:a9b725202132 draft
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 |
| files | data_manager/novocraft_index_builder.py data_manager_conf.xml |
| diffstat | 2 files changed, 6 insertions(+), 15 deletions(-) [+] |
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--- a/data_manager/novocraft_index_builder.py Sat Mar 05 10:29:02 2016 -0500 +++ b/data_manager/novocraft_index_builder.py Mon Mar 07 02:27:51 2016 -0500 @@ -37,26 +37,19 @@ elif not os.path.exists(target_directory): os.mkdir(target_directory) - if 'GALAXY_SLOTS' in os.environ: - nslots = os.environ['GALAXY_SLOTS'] - else: - nslots = 1 + index_filename = os.path.join(target_directory,"%.nix" % sequence_id) + cmdline_str = 'novoindex {} {}'.format(index_filename, fasta_filename) + cmdline = shlex.split(cmdline_str) - #cmdline_str = 'STAR --runMode genomeGenerate --genomeDir {} --genomeFastaFiles {} --runThreadN {}'.format( - # target_directory, - # fasta_filename, - # nslots) - #cmdline = shlex.split(cmdline_str) - index_filename = 'foo' - cmdline = ('touch', '{}/{}'.format(target_directory, index_filename)) + #index_filename = 'foo' + #cmdline = ('touch', '{}/{}'.format(target_directory, index_filename)) try: check_call(cmdline) except CalledProcessError: print("Error building RNA STAR index", file=sys.stderr) - data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=os.path.join(target_directory, index_filename) ) + data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=index_filename ) _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) - return ( index_filename ) def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ): data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
--- a/data_manager_conf.xml Sat Mar 05 10:29:02 2016 -0500 +++ b/data_manager_conf.xml Mon Mar 07 02:27:51 2016 -0500 @@ -8,9 +8,7 @@ <column name="name" /> <column name="path" output_ref="out_file"> <move type="file"> - <!--<move type="directory" relative_symlinks="True"> --> <!-- no need to set source, gets taken from out_dir.extra_files_path --> - <source>${path}</source> <!-- File name within the extra files path --> <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/novocraft_index/${value}</target> </move> <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/{$dbkey}/novocraft_index/${value}/${path}</value_translation>