# HG changeset patch # User bebatut # Date 1497271306 14400 # Node ID 3c14e5982438767de873a5d55ba36aead3697fc4 # Parent bbbcaf67e9fc1fdafc5005aac1dd24d906a0e902 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sortmerna_database_downloader commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty diff -r bbbcaf67e9fc -r 3c14e5982438 data_manager/data_manager_sortmerna_download.py --- 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): diff -r bbbcaf67e9fc -r 3c14e5982438 data_manager_conf.xml --- 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 @@ ${path} + rRNA_databases/${name} + + + ${path}.fasta rRNA_databases/${name}.fasta ${GALAXY_DATA_MANAGER_DATA_PATH}/rRNA_databases/${name}.fasta