Mercurial > repos > sanbi-uwc > data_manager_novocraft_index_builder
changeset 12:283eec05d1de draft
planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit e14dbfe322e3787d1ec9b7467a3677b101784227
| author | sanbi-uwc |
|---|---|
| date | Tue, 08 Mar 2016 05:38:52 -0500 |
| parents | a9b725202132 |
| children | 7014d5b1a9f4 |
| files | data_manager/novocraft_index_builder.py data_manager_conf.xml |
| diffstat | 2 files changed, 6 insertions(+), 5 deletions(-) [+] |
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--- a/data_manager/novocraft_index_builder.py Mon Mar 07 02:27:51 2016 -0500 +++ b/data_manager/novocraft_index_builder.py Tue Mar 08 05:38:52 2016 -0500 @@ -37,13 +37,14 @@ elif not os.path.exists(target_directory): os.mkdir(target_directory) - index_filename = os.path.join(target_directory,"%.nix" % sequence_id) + print(sequence_id) + nix_file = sequence_id + ".nix" + index_filename = os.path.join(target_directory, nix_file) cmdline_str = 'novoindex {} {}'.format(index_filename, fasta_filename) cmdline = shlex.split(cmdline_str) - #index_filename = 'foo' - #cmdline = ('touch', '{}/{}'.format(target_directory, index_filename)) try: + print(cmdline) check_call(cmdline) except CalledProcessError: print("Error building RNA STAR index", file=sys.stderr) @@ -83,7 +84,7 @@ params = loads(open(filename).read()) target_directory = params['output_data'][0]['extra_files_path'] - os.makedirs(target_directory) + #os.makedirs(target_directory) data_manager_dict = {} dbkey, sequence_id, sequence_name = get_dbkey_id_name(params, dbkey_description=args.dbkey_description)
--- a/data_manager_conf.xml Mon Mar 07 02:27:51 2016 -0500 +++ b/data_manager_conf.xml Tue Mar 08 05:38:52 2016 -0500 @@ -11,7 +11,7 @@ <!-- no need to set source, gets taken from out_dir.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}/${path}</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/novocraft_index/${value}/</value_translation> <value_translation type="function">abspath</value_translation> </column> </output>