Mercurial > repos > bebatut > data_manager_sortmerna_database_downloader
changeset 6:3c14e5982438 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sortmerna_database_downloader commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
| author | bebatut |
|---|---|
| date | Mon, 12 Jun 2017 08:41:46 -0400 |
| parents | bbbcaf67e9fc |
| children | d354679030fe |
| files | data_manager/data_manager_sortmerna_download.py data_manager_conf.xml |
| diffstat | 2 files changed, 7 insertions(+), 2 deletions(-) [+] |
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--- a/data_manager/data_manager_sortmerna_download.py Mon Jun 12 08:06:07 2017 -0400 +++ b/data_manager/data_manager_sortmerna_download.py Mon Jun 12 08:41:46 2017 -0400 @@ -130,9 +130,10 @@ # Move file os.rename(input_filepath, output_filepath) # Index the file with indexdb_rna + indexed_filepath = os.path.splitext(output_filepath)[0] command = "indexdb_rna --ref %s,%s" % ( output_filepath, - os.path.splitext(output_filepath)[0]) + indexed_filepath) process = subprocess.call(command, shell=True ) # Add entry in the data table db_name = os.path.splitext(filename)[0] @@ -142,7 +143,7 @@ dict( value="%s-%s" %(version, db_name), name=db_name, - path=output_filepath)) + path=indexed_filepath)) def download_db(data_tables, version, target_dir):
--- a/data_manager_conf.xml Mon Jun 12 08:06:07 2017 -0400 +++ b/data_manager_conf.xml Mon Jun 12 08:41:46 2017 -0400 @@ -8,6 +8,10 @@ <column name="path" output_ref="out_file" > <move type="file"> <source>${path}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">rRNA_databases/${name}</target> + </move> + <move type="file"> + <source>${path}.fasta</source> <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">rRNA_databases/${name}.fasta</target> </move> <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/rRNA_databases/${name}.fasta</value_translation>