# HG changeset patch
# User devteam
# Date 1429708297 14400
# Node ID d5d803e654dd005043746d7f9b6c916c45360faf
Uploaded
diff -r 000000000000 -r d5d803e654dd data_manager/kraken_database_builder.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/kraken_database_builder.xml Wed Apr 22 09:11:37 2015 -0400
@@ -0,0 +1,46 @@
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+ database builder
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+ kraken
+ jellyfish
+ KRAKEN_SCRIPT_PATH
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+ kraken -version | awk '{print $NF}'
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+ 10.1186/gb-2014-15-3-r46
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\ No newline at end of file
diff -r 000000000000 -r d5d803e654dd data_manager/make_json.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/make_json.py Wed Apr 22 09:11:37 2015 -0400
@@ -0,0 +1,28 @@
+import json
+import argparse
+import os
+import shutil
+
+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()
+
+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))
+
+if __name__ == '__main__':
+ main(args)
+
diff -r 000000000000 -r d5d803e654dd data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Wed Apr 22 09:11:37 2015 -0400
@@ -0,0 +1,18 @@
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diff -r 000000000000 -r d5d803e654dd tool-data/kraken_databases.loc.sample
diff -r 000000000000 -r d5d803e654dd tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Wed Apr 22 09:11:37 2015 -0400
@@ -0,0 +1,8 @@
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diff -r 000000000000 -r d5d803e654dd tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Wed Apr 22 09:11:37 2015 -0400
@@ -0,0 +1,12 @@
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+ $REPOSITORY_INSTALL_DIR
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