# HG changeset patch
# User dfornika
# Date 1551318153 18000
# Node ID b1805f086b662b3385439d895dfd47fc538d3100
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 9b4d704c147761201fa9f1450fcf5ba6871104d8-dirty
diff -r 000000000000 -r b1805f086b66 data_manager/kraken2_database_builder.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/kraken2_database_builder.xml Wed Feb 27 20:42:33 2019 -0500
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+ database builder
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+ kraken2
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+ kraken2 -version | head -n 1 | awk '{print $NF}'
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+ 10.1186/gb-2014-15-3-r46
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diff -r 000000000000 -r b1805f086b66 data_manager/kraken2_standard_database_builder.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/kraken2_standard_database_builder.xml Wed Feb 27 20:42:33 2019 -0500
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+ database builder
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+ kraken2
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+ kraken2 -version | head -n 1 | awk '{print $NF}'
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+ 10.1186/gb-2014-15-3-r46
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diff -r 000000000000 -r b1805f086b66 data_manager/make_json.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/make_json.py Wed Feb 27 20:42:33 2019 -0500
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+import argparse
+import json
+import os
+import shutil
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+def main(args):
+ data_manager_entry = {}
+ data_manager_entry['value'] = args.database.lower()
+ data_manager_entry['name'] = args.database
+ data_manager_entry['path'] = '.'
+ data_manager_json = dict(data_tables=dict(kraken_databases=data_manager_entry))
+ params = json.loads(open(args.output).read())
+ target_directory = params['output_data'][0]['extra_files_path']
+ os.mkdir(target_directory)
+ output_path = os.path.join(os.getcwd(), 'kraken-database')
+ for filename in os.listdir(output_path):
+ shutil.move(os.path.join(output_path, filename), target_directory)
+ file(args.output, 'w').write(json.dumps(data_manager_json))
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+if __name__ == '__main__':
+ parser = argparse.ArgumentParser(description='Create data manager json.')
+ parser.add_argument('--db', dest='database', action='store', help='Database name')
+ parser.add_argument('--out', dest='output', action='store', help='JSON filename')
+ args = parser.parse_args()
+ main(args)
diff -r 000000000000 -r b1805f086b66 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Wed Feb 27 20:42:33 2019 -0500
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