# HG changeset patch
# User dfornika
# Date 1551395975 18000
# Node ID c6db7ff0b3f839998f9375dd93e15769e6c3e2fd
# Parent 25298e35048f828059479e722168930f06d8fa98
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit f05f93ee024df8b38efa1c92db9785d52c726f85-dirty
diff -r 25298e35048f -r c6db7ff0b3f8 data_manager/kraken2_build_custom.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/kraken2_build_custom.py Thu Feb 28 18:19:35 2019 -0500
@@ -0,0 +1,117 @@
+#!/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
+
+from pprint import pprint
+
+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(data_manager_dict, kraken2_args, params, target_directory, data_table_name=DATA_TABLE_NAME):
+ today = datetime.date.today().isoformat()
+ database_name = "_".join([today, "custom"])
+
+ args = [
+ 'kraken2-build',
+ '--threads', str(kraken2_args["threads"]),
+ '--download-taxonomy',
+ '--db', database_name
+ ]
+
+ run(args, target_directory)
+
+ args = [
+ 'kraken2-build',
+ '--threads', str(kraken2_args["threads"]),
+ '--add-to-library', kraken2_args["fasta"],
+ '--db', database_name
+ ]
+
+ run(args, target_directory)
+
+ args = [
+ 'kraken2-build',
+ '--threads', str(kraken2_args["threads"]),
+ '--clean',
+ '--db', database_name
+ ]
+
+ run(args, target_directory)
+
+ data_table_entry = {
+ "value": database_name,
+ "name": database_name,
+ "path": database_name
+ }
+
+ _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
+
+
+def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):
+ 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('params')
+ 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 = {
+ "kmer_len": args.kmer_len,
+ "minimizer_len": args.minimizer_len,
+ "minimizer_spaces": args.minimizer_spaces,
+ "fasta": args.fasta,
+ "threads": args.threads,
+ }
+
+ params = json.loads(open(args.params).read())
+ pprint(params)
+ target_directory = params['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
+
+ data_manager_dict = {}
+
+ # build the index
+ kraken2_build(
+ data_manager_dict,
+ kraken2_args,
+ params,
+ target_directory
+ )
+
+ # save info to json file
+ open(args.params, 'wb').write(json.dumps(data_manager_dict))
+
+
+if __name__ == "__main__":
+ main()
diff -r 25298e35048f -r c6db7ff0b3f8 data_manager/kraken2_build_custom.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/kraken2_build_custom.xml Thu Feb 28 18:19:35 2019 -0500
@@ -0,0 +1,33 @@
+
+
+ database builder
+
+ kraken2
+
+ kraken2 -version | head -n 1 | awk '{print $NF}'
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 10.1186/gb-2014-15-3-r46
+
+
diff -r 25298e35048f -r c6db7ff0b3f8 data_manager/kraken2_build_standard.py
--- a/data_manager/kraken2_build_standard.py Thu Feb 28 01:50:00 2019 -0500
+++ b/data_manager/kraken2_build_standard.py Thu Feb 28 18:19:35 2019 -0500
@@ -27,13 +27,22 @@
'--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
'--db', database_name
]
- pprint(args)
proc = subprocess.Popen(args=args, shell=False, cwd=target_directory)
return_code = proc.wait()
if return_code:
print("Error building database.", file=sys.stderr)
sys.exit( return_code )
-
+ args = [
+ 'kraken2-build',
+ '--threads', str(kraken2_args["threads"]),
+ '--clean',
+ '--db', database_name
+ ]
+ proc = subprocess.Popen(args=args, shell=False, cwd=target_directory)
+ return_code = proc.wait()
+ if return_code:
+ print("Error building database.", file=sys.stderr)
+ sys.exit( return_code )
data_table_entry = {
"value": database_name,
"name": database_name,
diff -r 25298e35048f -r c6db7ff0b3f8 tool-data/kraken2_databases.loc.sample
diff -r 25298e35048f -r c6db7ff0b3f8 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Thu Feb 28 18:19:35 2019 -0500
@@ -0,0 +1,8 @@
+
+
+
+
+