# HG changeset patch
# User dfornika
# Date 1551745233 18000
# Node ID ae6180bdb1e931f18d4696840e5dc8b6e2e084bc
# Parent ce101123d0154462df05245def702de0ca4c0ea1
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 70494d589aa1990618ebc7a895e91477d41c3203-dirty
diff -r ce101123d015 -r ae6180bdb1e9 data_manager/kraken2_build_special.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/kraken2_build_special.py Mon Mar 04 19:20:33 2019 -0500
@@ -0,0 +1,109 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import argparse
+import datetime
+import errno
+import json
+import os
+import string
+import subprocess
+import sys
+
+
+DATA_TABLE_NAME = "kraken2_databases"
+
+def run(args, cwd):
+ proc = subprocess.Popen(args=args, shell=False, cwd=cwd)
+ return_code = proc.wait()
+ if return_code:
+ print("Error building database.", file=sys.stderr)
+ 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,
+ kraken2_args["special"],
+ "kmer-len=" + str(kraken2_args["kmer_len"]),
+ "minimizer-len=" + str(kraken2_args["minimizer_len"]),
+ "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]),
+ ])
+
+ args = [
+ '--threads', str(kraken2_args["threads"]),
+ '--special', kraken2_args["special"]
+ '--kmer-len', str(kraken2_args["kmer_len"]),
+ '--minimizer-len', str(kraken2_args["minimizer_len"]),
+ '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
+ '--db', database_name
+ ]
+
+ run(['kraken2-build'] + args, target_directory)
+
+ args = [
+ '--threads', str(kraken2_args["threads"]),
+ '--clean',
+ '--db', database_name
+ ]
+
+ run(['kraken2-build'] + args, target_directory)
+
+ data_table_entry = {
+ "value": database_name,
+ "name": database_name,
+ "path": database_name
+ }
+
+ _add_data_table_entry(data_manager_dict, data_table_entry)
+
+
+def _add_data_table_entry(data_manager_dict, data_table_entry, data_table_name=DATA_TABLE_NAME):
+ data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
+ data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get( data_table_name, [] )
+ data_manager_dict['data_tables'][data_table_name].append( data_table_entry )
+ return data_manager_dict
+
+
+def main():
+ parser = argparse.ArgumentParser()
+ parser.add_argument('data_manager_json')
+ parser.add_argument( '-b', '--db-type', dest='db_type', help='database type (one of: silva, rdp, greengenes)' )
+ parser.add_argument( '-k', '--kmer-len', dest='kmer_len', type=int, default=35, help='kmer length' )
+ parser.add_argument( '-m', '--minimizer-len', dest='minimizer_len', type=int, default=31, help='minimizer length' )
+ parser.add_argument( '-s', '--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces' )
+ parser.add_argument( '-t', '--threads', dest='threads', default=1, help='threads' )
+ args = parser.parse_args()
+
+ kraken2_args = {
+ "special": args.db_type,
+ "kmer_len": args.kmer_len,
+ "minimizer_len": args.minimizer_len,
+ "minimizer_spaces": args.minimizer_spaces,
+ "threads": args.threads,
+ }
+
+ data_manager_input = json.loads(open(args.data_manager_json).read())
+
+ target_directory = data_manager_input['output_data'][0]['extra_files_path']
+
+ try:
+ os.mkdir( target_directory )
+ except OSError as exc:
+ if exc.errno == errno.EEXIST and os.path.isdir( target_directory ):
+ pass
+ else:
+ raise
+
+ kraken2_build_standard(
+ data_manager_input,
+ kraken2_args,
+ target_directory,
+ )
+
+ open(args.data_manager_json, 'wb').write(json.dumps(data_manager_input))
+
+
+if __name__ == "__main__":
+ main()
diff -r ce101123d015 -r ae6180bdb1e9 data_manager/kraken2_build_special.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/kraken2_build_special.xml Mon Mar 04 19:20:33 2019 -0500
@@ -0,0 +1,37 @@
+
+
+ database builder
+
+ kraken2
+
+ kraken2 -version | head -n 1 | awk '{print $NF}'
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 10.1186/gb-2014-15-3-r46
+
+
diff -r ce101123d015 -r ae6180bdb1e9 data_manager/kraken2_build_standard.py
--- a/data_manager/kraken2_build_standard.py Mon Mar 04 19:01:17 2019 -0500
+++ b/data_manager/kraken2_build_standard.py Mon Mar 04 19:20:33 2019 -0500
@@ -42,7 +42,6 @@
run(['kraken2-build'] + args, target_directory)
args = [
- 'kraken2-build',
'--threads', str(kraken2_args["threads"]),
'--clean',
'--db', database_name
diff -r ce101123d015 -r ae6180bdb1e9 data_manager_conf.xml
--- a/data_manager_conf.xml Mon Mar 04 19:01:17 2019 -0500
+++ b/data_manager_conf.xml Mon Mar 04 19:20:33 2019 -0500
@@ -29,4 +29,19 @@
+
+
+
+
+