| Previous changeset 68:2650a19fe260 (2021-11-04) Next changeset 70:93b67ce30fcf (2021-11-05) |
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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 cec255ceca4b1dd39c4b5795cbfcf5f8e74fc9c7-dirty" |
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modified:
data_manager/kraken2_build_database.py data_manager/kraken2_build_database.xml |
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| diff -r 2650a19fe260 -r 37467f9b7ea3 data_manager/kraken2_build_database.py --- a/data_manager/kraken2_build_database.py Thu Nov 04 17:25:24 2021 +0000 +++ b/data_manager/kraken2_build_database.py Fri Nov 05 18:55:37 2021 +0000 |
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| @@ -51,6 +51,13 @@ return self.value +class PrebuiltDate(Enum): + date_20210517 = '2021-05-17' + date_20201202 = '2020-12-02' + + def __str__(self): + return self.value + class StandardPrebuiltSizes(Enum): full = 'full' gb_16 = '16' @@ -119,6 +126,7 @@ return data_table_entry + def kraken2_build_standard_prebuilt(standard_prebuilt_size, target_directory, data_table_name=DATA_TABLE_NAME): now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ") @@ -137,13 +145,14 @@ ]) database_path = database_value - + size_to_url_str = { 'full': '', '16': '_16gb', '8': '_8gb', } - date_url_str = '20210517' + # we may need to let the user choose the date when new DBs are posted. + date_url_str = args.prebuilt_date.replace('-', '') standard_prebuilt_size_url = size_to_url_str[standard_prebuilt_size] # download the pre-built database src = urlopen( @@ -357,7 +366,8 @@ 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)') - parser.add_argument('--standard-prebuilt-size', dest='standard_prebuilt_size', type=StandardPrebuiltSizes, choices=list(StandardPrebuiltSizes), help='Size of standard prebuilt database to download (only applies to --database-type standard_prebuilt)') + parser.add_argument('--standard-prebuilt-size', dest='standard_prebuilt_size', type=StandardPrebuiltSizes, choices=list(StandardPrebuiltSizes), help='Size of standard prebuilt database to download (only applies to --database-type standard_prebuilt. Options are: "8", "16", "full".)') + parser.add_argument('--prebuilt-date', dest='prebuilt_date', type=PrebuiltDates, choices=list(PrebuiltDates), help='Database build date (YYYY-MM-DD). Only applies to --database-type standard_prebuilt. Options are: "2021-05-17", "2020-12-02".)') parser.add_argument('--special-database-type', dest='special_database_type', type=SpecialDatabaseTypes, choices=list(SpecialDatabaseTypes), help='type of special database to build (only applies to --database-type special)') parser.add_argument('--custom-fasta', dest='custom_fasta', help='fasta file for custom database (only applies to --database-type custom)') parser.add_argument('--custom-database-name', dest='custom_database_name', help='Name for custom database (only applies to --database-type custom)') |
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| diff -r 2650a19fe260 -r 37467f9b7ea3 data_manager/kraken2_build_database.xml --- a/data_manager/kraken2_build_database.xml Thu Nov 04 17:25:24 2021 +0000 +++ b/data_manager/kraken2_build_database.xml Fri Nov 05 18:55:37 2021 +0000 |
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| @@ -65,11 +65,15 @@ <when value="standard_local_build"> <expand macro="common_params" /> </when> - <when value="standard_prebuilt"> + <when value="standard_prebuilt"> <param name="standard_prebuilt_size" type="select" multiple="false" label="Select size of prebuilt database to download"> - <option value="full">Full (~50 GB)</option> + <option value="full">Standard-Full (~50 GB)</option> <option value="16">Standard-16 (~16 GB)</option> - <option value="8">Standard-8 (~8 GB)</option> + <option value="8">Standard-8 (~8 GB)</option> + </param> + <param name="standard_prebuilt_date" type="select" multiple="false" label="Select database build date"> + <option value="2021-05-27">May 27, 2021</option> + <option value="2020-12-02">December 2, 2020</option> </param> </when> <when value="minikraken"> |