Mercurial > repos > dfornika > data_manager_build_bracken_database
changeset 7:cc49eb0defee draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_bracken_database/ commit 324b55b24e9d403b04a1cc6aba362b03bad98368-dirty
| author | dfornika |
|---|---|
| date | Wed, 31 Jul 2019 19:09:09 -0400 |
| parents | f25264bb7d6d |
| children | 891f564fd6e3 |
| files | data_manager/bracken_build_database.py data_manager/bracken_build_database.xml data_manager_conf.xml |
| diffstat | 3 files changed, 5 insertions(+), 22 deletions(-) [+] |
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--- a/data_manager/bracken_build_database.py Wed Jul 31 18:08:06 2019 -0400 +++ b/data_manager/bracken_build_database.py Wed Jul 31 19:09:09 2019 -0400 @@ -25,15 +25,7 @@ database_name = database_name - database_path = bracken_build_args['kraken_database'] - - try: - os.mkdir( os.path.join(target_directory, database_path) ) - except OSError as exc: - if exc.errno == errno.EEXIST and os.path.isdir( os.path.join(target_directory, database_path) ): - pass - else: - raise + database_path = os.path.join(bracken_build_args['kraken_database'], 'database' + str(bracken_build_args['read_len']) + 'mers.kmer_distrib') bracken_build_args_list = [ @@ -43,8 +35,7 @@ '-d', bracken_build_args['kraken_database'], ] - subprocess.check_call(['bracken-build'] + bracken_build_args_list, - cwd=os.path.join(target_directory, database_path)) + subprocess.check_call(['bracken-build'] + bracken_build_args_list) data_table_entry = { @@ -53,7 +44,7 @@ { "value": database_value, "name": database_name, - "path": os.path.join(database_path), + "path": database_path, } ] }
--- a/data_manager/bracken_build_database.xml Wed Jul 31 18:08:06 2019 -0400 +++ b/data_manager/bracken_build_database.xml Wed Jul 31 19:09:09 2019 -0400 @@ -4,14 +4,13 @@ <requirements> <requirement type="package" version="2.2">bracken</requirement> <requirement type="package" version="2.0.8_beta">kraken2</requirement> - <requirement type="package" version="1.7.0">bagit</requirement> </requirements> <version_command>bracken --version</version_command> <command detect_errors="exit_code"> <![CDATA[ python '$__tool_directory__/bracken_build_database.py' '${out_file}' - --kraken-db ${kraken_db} + --kraken-db ${kraken_db.fields.path} --threads \${GALAXY_SLOTS:-1} --kmer-len ${kmer_len} --read-len ${read_len}
--- a/data_manager_conf.xml Wed Jul 31 18:08:06 2019 -0400 +++ b/data_manager_conf.xml Wed Jul 31 19:09:09 2019 -0400 @@ -4,14 +4,7 @@ <output> <column name="value"/> <column name="name"/> - <column name="path" output_ref="out_file"> - <move type="file"> - <source>${path}</source> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">bracken_databases/${path}</target> - </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/bracken_databases/${path}</value_translation> - <value_translation type="function">abspath</value_translation> - </column> + <column name="path" output_ref="out_file"/> </output> </data_table> </data_manager>