| Previous changeset 62:38c99b294264 (2019-10-23) Next changeset 64:e5eba596cc1b (2021-11-03) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3-dirty" |
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modified:
data_manager/kraken2_build_database.py data_manager/kraken2_build_database.xml data_manager_conf.xml test-data/kraken2_custom_data_manager.json |
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| diff -r 38c99b294264 -r 80e778af6c6c data_manager/kraken2_build_database.py --- a/data_manager/kraken2_build_database.py Wed Oct 23 14:18:06 2019 -0400 +++ b/data_manager/kraken2_build_database.py Wed Nov 03 22:34:28 2021 +0000 |
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| @@ -59,6 +59,7 @@ "kmer-len", str(kraken2_args["kmer_len"]), "minimizer-len", str(kraken2_args["minimizer_len"]), "minimizer-spaces", str(kraken2_args["minimizer_spaces"]), + "load-factor", str(kraken2_args["load_factor"]), ]) database_name = " ".join([ @@ -68,6 +69,7 @@ "kmer-len=" + str(kraken2_args["kmer_len"]) + ",", "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",", "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")", + "load-factor", str(kraken2_args["load_factor"]), ]) database_path = database_value @@ -78,6 +80,7 @@ '--kmer-len', str(kraken2_args["kmer_len"]), '--minimizer-len', str(kraken2_args["minimizer_len"]), '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]), + '--load-factor', str(kraken2_args["load_factor"]), '--db', database_path ] @@ -129,7 +132,7 @@ # download the minikraken2 data src = urlopen( - 'ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken2_%s_8GB_201904_UPDATE.tgz' + 'https://genome-idx.s3.amazonaws.com/kraken/minikraken2_%s_8GB_201904.tgz' % minikraken2_version ) with open('tmp_data.tar.gz', 'wb') as dst: @@ -172,6 +175,7 @@ "kmer-len", str(kraken2_args["kmer_len"]), "minimizer-len", str(kraken2_args["minimizer_len"]), "minimizer-spaces", str(kraken2_args["minimizer_spaces"]), + "load-factor", str(kraken2_args["load_factor"]), ]) database_name = " ".join([ @@ -181,6 +185,7 @@ "kmer-len=" + str(kraken2_args["kmer_len"]) + ",", "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",", "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")", + "load-factor=" + str(kraken2_args["load_factor"]) + ")", ]) database_path = database_value @@ -191,6 +196,7 @@ '--kmer-len', str(kraken2_args["kmer_len"]), '--minimizer-len', str(kraken2_args["minimizer_len"]), '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]), + '--load-factor', str(kraken2_args["load_factor"]), '--db', database_path ] @@ -247,6 +253,7 @@ '--kmer-len', str(kraken2_args["kmer_len"]), '--minimizer-len', str(kraken2_args["minimizer_len"]), '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]), + '--load-factor', str(kraken2_args["load_factor"]), '--db', custom_database_name ] @@ -282,6 +289,7 @@ parser.add_argument('--kmer-len', dest='kmer_len', type=int, default=35, help='kmer length') parser.add_argument('--minimizer-len', dest='minimizer_len', type=int, default=31, help='minimizer length') parser.add_argument('--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces') + parser.add_argument('--load-factor', dest='load_factor', type=float, default=0.7, help='load factor') parser.add_argument('--threads', dest='threads', default=1, help='threads') parser.add_argument('--database-type', dest='database_type', type=KrakenDatabaseTypes, choices=list(KrakenDatabaseTypes), required=True, help='type of kraken database to build') parser.add_argument('--minikraken2-version', dest='minikraken2_version', type=Minikraken2Versions, choices=list(Minikraken2Versions), help='MiniKraken2 version (only applies to --database-type minikraken)') @@ -292,14 +300,15 @@ parser.add_argument('--clean', dest='clean', action='store_true', help='Clean up extra files') args = parser.parse_args() - data_manager_input = json.loads(open(args.data_manager_json).read()) + with open(args.data_manager_json) as fh: + data_manager_input = json.load(fh) target_directory = data_manager_input['output_data'][0]['extra_files_path'] try: - os.mkdir( target_directory ) + os.mkdir(target_directory) except OSError as exc: - if exc.errno == errno.EEXIST and os.path.isdir( target_directory ): + if exc.errno == errno.EEXIST and os.path.isdir(target_directory): pass else: raise @@ -311,6 +320,7 @@ "kmer_len": args.kmer_len, "minimizer_len": args.minimizer_len, "minimizer_spaces": args.minimizer_spaces, + "load_factor": args.load_factor, "threads": args.threads, "clean": args.clean, } @@ -329,6 +339,7 @@ "kmer_len": args.kmer_len, "minimizer_len": args.minimizer_len, "minimizer_spaces": args.minimizer_spaces, + "load_factor": args.load_factor, "threads": args.threads, "clean": args.clean, } @@ -343,6 +354,7 @@ "kmer_len": args.kmer_len, "minimizer_len": args.minimizer_len, "minimizer_spaces": args.minimizer_spaces, + "load_factor": args.load_factor, "threads": args.threads, "clean": args.clean, } @@ -354,7 +366,8 @@ else: sys.exit("Invalid database type") - open(args.data_manager_json, 'w').write(json.dumps(data_manager_output)) + with open(args.data_manager_json, 'w') as fh: + json.dump(data_manager_output, fh, sort_keys=True) if __name__ == "__main__": |
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| diff -r 38c99b294264 -r 80e778af6c6c data_manager/kraken2_build_database.xml --- a/data_manager/kraken2_build_database.xml Wed Oct 23 14:18:06 2019 -0400 +++ b/data_manager/kraken2_build_database.xml Wed Nov 03 22:34:28 2021 +0000 |
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| @@ -1,16 +1,19 @@ <?xml version="1.0"?> -<tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="2.0.8_beta_galaxy1"> +<tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="@TOOL_VERSION@" profile="18.09"> <macros> + <token name="@TOOL_VERSION@">2.1.1</token> <xml name="common_params"> <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" /> <param name="minimizer_len" type="integer" value="31" label="Minimizer length" /> <param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" /> + <param name="load_factor" type="float" value="0.7" min="0" max="1" label="Load factor" help="Proportion of the hash table to be populated" /> <param name="clean" type="boolean" truevalue="--clean" falsevalue="" checked="true" label="Clean up extra files" /> </xml> </macros> <description>database builder</description> <requirements> - <requirement type="package" version="2.0.8_beta">kraken2</requirement> + <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement> + <requirement type="package" version="3.7">python</requirement> </requirements> <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command> <command detect_errors="exit_code"> @@ -25,6 +28,7 @@ --kmer-len ${database_type.kmer_len} --minimizer-len ${database_type.minimizer_len} --minimizer-spaces ${database_type.minimizer_spaces} + --load-factor ${database_type.load_factor} ${database_type.clean} #else if $database_type.database_type == "special" --threads \${GALAXY_SLOTS:-1} @@ -32,6 +36,7 @@ --kmer-len ${database_type.kmer_len} --minimizer-len ${database_type.minimizer_len} --minimizer-spaces ${database_type.minimizer_spaces} + --load-factor ${database_type.load_factor} ${database_type.clean} #else if $database_type.database_type == "custom" --threads \${GALAXY_SLOTS:-1} @@ -41,6 +46,7 @@ --kmer-len ${database_type.kmer_len} --minimizer-len ${database_type.minimizer_len} --minimizer-spaces ${database_type.minimizer_spaces} + --load-factor ${database_type.load_factor} ${database_type.clean} #end if ]]> |
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| diff -r 38c99b294264 -r 80e778af6c6c data_manager_conf.xml --- a/data_manager_conf.xml Wed Oct 23 14:18:06 2019 -0400 +++ b/data_manager_conf.xml Wed Nov 03 22:34:28 2021 +0000 |
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| @@ -1,5 +1,5 @@ <data_managers> - <data_manager tool_file="data_manager/kraken2_build_database.xml" id="kraken2_build_database" version="2.0.8_beta_galaxy1"> + <data_manager tool_file="data_manager/kraken2_build_database.xml" id="kraken2_build_database" version="2.0.8_beta+galaxy1"> <data_table name="kraken2_databases"> <output> <column name="value"/> |
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| diff -r 38c99b294264 -r 80e778af6c6c test-data/kraken2_custom_data_manager.json --- a/test-data/kraken2_custom_data_manager.json Wed Oct 23 14:18:06 2019 -0400 +++ b/test-data/kraken2_custom_data_manager.json Wed Nov 03 22:34:28 2021 +0000 |
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| @@ -1,1 +1,1 @@ -{"data_tables": {"kraken2_databases": [{"path": "database", "name": "database", "value": "database"}]}} \ No newline at end of file +{"data_tables": {"kraken2_databases": [{"name": "database", "path": "database", "value": "database"}]}} \ No newline at end of file |