Mercurial > repos > dfornika > data_manager_build_kraken2_database
diff data_manager/kraken2_build_special.py @ 11:1dc93ae264e6 draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 70494d589aa1990618ebc7a895e91477d41c3203-dirty
author | dfornika |
---|---|
date | Tue, 05 Mar 2019 14:33:23 -0500 |
parents | 1601703ae511 |
children | 039a65ff445d |
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--- a/data_manager/kraken2_build_special.py Mon Mar 04 20:31:23 2019 -0500 +++ b/data_manager/kraken2_build_special.py Tue Mar 05 14:33:23 2019 -0500 @@ -22,14 +22,33 @@ sys.exit( return_code ) def kraken2_build_standard(data_manager_dict, kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME): - today = datetime.date.today().isoformat() - database_name = "_".join([ - today, + + now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ") + + special_database_names = { + "rdp": "RDP", + "greengenes": "Greengenes", + "silva": "Silva", + } + + database_value = "_".join([ + now, kraken2_args["special"], - "kmer-len=" + str(kraken2_args["kmer_len"]), - "minimizer-len=" + str(kraken2_args["minimizer_len"]), - "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]), + "kmer-len", str(kraken2_args["kmer_len"]), + "minimizer-len", str(kraken2_args["minimizer_len"]), + "minimizer-spaces", str(kraken2_args["minimizer_spaces"]), ]) + + database_name = " ".join([ + special_database_names[kraken2_args["special"]], + "(Created:", + now + "," + "kmer-len=" + str(kraken2_args["kmer_len"]) + ",", + "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",", + "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")", + ]) + + database_path = database_value args = [ '--threads', str(kraken2_args["threads"]), @@ -37,7 +56,7 @@ '--kmer-len', str(kraken2_args["kmer_len"]), '--minimizer-len', str(kraken2_args["minimizer_len"]), '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]), - '--db', database_name + '--db', database_path ] run(['kraken2-build'] + args, target_directory) @@ -45,15 +64,15 @@ args = [ '--threads', str(kraken2_args["threads"]), '--clean', - '--db', database_name + '--db', database_path ] run(['kraken2-build'] + args, target_directory) data_table_entry = { - "value": database_name, + "value": database_value, "name": database_name, - "path": database_name + "path": database_path, } _add_data_table_entry(data_manager_dict, data_table_entry)