Mercurial > repos > dfornika > pathogist
changeset 10:84c2f132bb99 draft
planemo upload for repository https://github.com/dfornika/tools-pathogist/tree/master/tools
| author | dfornika |
|---|---|
| date | Thu, 05 Oct 2017 20:18:03 -0400 |
| parents | d6f4ba9bf576 |
| children | ccd01975863b |
| files | data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.py |
| diffstat | 1 files changed, 3 insertions(+), 1 deletions(-) [+] |
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--- a/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.py Thu Oct 05 20:12:38 2017 -0400 +++ b/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.py Thu Oct 05 20:18:03 2017 -0400 @@ -12,7 +12,9 @@ def build_mentalist_database( data_manager_dict, database_name, kmer_size, profile, fasta_files, params, target_directory, data_table_names=DEFAULT_DATA_TABLE_NAMES ): - args = [ 'mentalist', 'build_db', '--db', database_name, '-k', str(kmer_size), '--profile', profile, '--fasta_files', " ".join(fasta_files)] + args = [ 'mentalist', 'build_db', '--db', database_name, '-k', str(kmer_size), '--fasta_files', " ".join(fasta_files)] + if profile: + args += ['--profile', profile] print(args) proc = subprocess.Popen( args=args, shell=False, cwd=target_directory ) return_code = proc.wait()