Mercurial > repos > ieguinoa > data_manager_salmon_index_builder
changeset 5:3888ec1918d0 draft
Uploaded
| author | ieguinoa |
|---|---|
| date | Thu, 03 Jan 2019 10:51:18 -0500 |
| parents | ef2031036f47 |
| children | d22f69a2e80e |
| files | data_manager/salmon_index_builder.py data_manager_conf.xml |
| diffstat | 2 files changed, 5 insertions(+), 3 deletions(-) [+] |
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--- a/data_manager/salmon_index_builder.py Mon Nov 26 10:53:58 2018 -0500 +++ b/data_manager/salmon_index_builder.py Thu Jan 03 10:51:18 2019 -0500 @@ -30,17 +30,19 @@ target_directory = params[ 'output_data' ][0]['extra_files_path'] if not os.path.exists( target_directory ): os.mkdir( target_directory ) + path=sequence_id args = [ 'salmon', 'index' ] if options.kmer_size != '': args.append('-k') args.append(options.kmer_size) + path=path + '_kmer_'+ options.kmer_size args.extend( [ '-t' , options.fasta_filename, '-i', target_directory ] ) proc = subprocess.Popen( args=args, shell=False) return_code = proc.wait() if return_code: print("Error building index.", file=sys.stderr) sys.exit( return_code ) - data_table_entry = dict( value=sequence_id, dbkey=options.fasta_dbkey, name=sequence_name, path=sequence_id ) + data_table_entry = dict( value=sequence_id, dbkey=options.fasta_dbkey, name=sequence_name, path=path ) _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
--- a/data_manager_conf.xml Mon Nov 26 10:53:58 2018 -0500 +++ b/data_manager_conf.xml Thu Jan 03 10:51:18 2019 -0500 @@ -9,9 +9,9 @@ <column name="path" output_ref="out_file" > <move type="directory" relativize_symlinks="True"> <!-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base --> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/salmon_index/${value}</target> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/salmon_index/${path}</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/salmon_index/${value}/${path}</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/salmon_index/${path}</value_translation> <value_translation type="function">abspath</value_translation> </column> </output>