| Previous changeset 21:fd3fd1cae8dd (2019-03-04) Next changeset 23:0c4e821c704b (2019-03-05) |
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Commit message:
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 70494d589aa1990618ebc7a895e91477d41c3203-dirty |
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modified:
data_manager/kraken2_build_special.py |
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| diff -r fd3fd1cae8dd -r 8e8de26a1383 data_manager/kraken2_build_special.py --- a/data_manager/kraken2_build_special.py Mon Mar 04 21:08:15 2019 -0500 +++ b/data_manager/kraken2_build_special.py Tue Mar 05 12:53:00 2019 -0500 |
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| @@ -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"]), ]) + + 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) |