# HG changeset patch
# User dfornika
# Date 1551816642 18000
# Node ID 7233538ef3cb41091502d90ed7ba3f5af563866e
# Parent 0c4e821c704b42a2907d998b879ed69f45f1d7dd
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 70494d589aa1990618ebc7a895e91477d41c3203-dirty
diff -r 0c4e821c704b -r 7233538ef3cb data_manager/kraken2_build_minikraken.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/kraken2_build_minikraken.py Tue Mar 05 15:10:42 2019 -0500
@@ -0,0 +1,104 @@
+#!/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_minikraken(data_manager_dict, minikraken2_version, target_directory, data_table_name=DATA_TABLE_NAME):
+
+ now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
+
+ database_value = "_".join([
+ now,
+ "minikraken2",
+ minikraken2_version,
+ "8GB",
+ ])
+
+ database_name = " ".join([
+ "Minikraken2",
+ minikraken2_version,
+ "(Created:",
+ now + ")"
+ ])
+
+ database_path = database_value
+
+ args = [
+ 'https://ccb.jhu.edu/software/kraken2/dl/minikraken2_' + minikraken2_version + '_8GB.tgz'
+ ]
+
+ run(['wget'] + args, target_directory)
+
+ args = [
+ '-xvzf', 'minikraken2_' + minikraken2_version + '_8GB.tgz'
+ ]
+
+ run(['tar'] + args, target_directory)
+
+ data_table_entry = {
+ "value": database_value,
+ "name": database_name,
+ "path": database_path,
+ }
+
+ _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( '-v', '--minikraken2-version', dest='minikraken2_version', default="v2", help='MiniKraken2 version (v1 or v2)' )
+ parser.add_argument( '-t', '--threads', dest='threads', default=1, help='threads' )
+
+ args = parser.parse_args()
+
+ 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
+
+ data_manager_output = {}
+
+ kraken2_build_minikraken(
+ data_manager_output,
+ args.minikraken2_version,
+ target_directory,
+ )
+
+ open(args.data_manager_json, 'wb').write(json.dumps(data_manager_output))
+
+
+if __name__ == "__main__":
+ main()
diff -r 0c4e821c704b -r 7233538ef3cb data_manager/kraken2_build_minikraken.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/kraken2_build_minikraken.xml Tue Mar 05 15:10:42 2019 -0500
@@ -0,0 +1,30 @@
+
+
+ database builder
+
+ kraken2
+
+ kraken2 -version | head -n 1 | awk '{print $NF}'
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 10.1186/gb-2014-15-3-r46
+
+
diff -r 0c4e821c704b -r 7233538ef3cb data_manager/kraken2_build_special.py
--- a/data_manager/kraken2_build_special.py Tue Mar 05 13:11:02 2019 -0500
+++ b/data_manager/kraken2_build_special.py Tue Mar 05 15:10:42 2019 -0500
@@ -42,7 +42,7 @@
database_name = " ".join([
special_database_names[kraken2_args["special"]],
"(Created:",
- now + ","
+ now + ",",
"kmer-len=" + str(kraken2_args["kmer_len"]) + ",",
"minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",",
"minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")",
diff -r 0c4e821c704b -r 7233538ef3cb data_manager/kraken2_build_standard.py
--- a/data_manager/kraken2_build_standard.py Tue Mar 05 13:11:02 2019 -0500
+++ b/data_manager/kraken2_build_standard.py Tue Mar 05 15:10:42 2019 -0500
@@ -22,21 +22,34 @@
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,
+ now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
+
+ database_value = "_".join([
+ now,
"standard",
- "kmer-len=" + str(kraken2_args["kmer_len"]),
- "minimizer-len=" + str(kraken2_args["minimizer_len"]),
- "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]),
+ "kmer-len" + str(kraken2_args["kmer_len"]),
+ "minimizer-len" + str(kraken2_args["minimizer_len"]),
+ "minimizer-spaces" + str(kraken2_args["minimizer_spaces"]),
])
+
+ database_name = " ".join([
+ "Standard",
+ "(Created:",
+ now + ",",
+ "kmer-len=" + str(kraken2_args["kmer_len"]) + ",",
+ "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",",
+ "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")",
+ ])
+
+ database_path = database_value
+
args = [
'--threads', str(kraken2_args["threads"]),
'--standard',
'--kmer-len', str(kraken2_args["kmer_len"]),
'--minimizer-len', str(kraken2_args["minimizer_len"]),
'--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
- '--db', database_name
+ '--db', database_path
]
run(['kraken2-build'] + args, target_directory)
@@ -44,15 +57,15 @@
args = [
'--threads', str(kraken2_args["threads"]),
'--clean',
- '--db', database_name
+ '--db', database_path
]
run(['kraken2-build'] + args, target_directory)
data_table_entry = {
- "value": database_name,
+ "value": database_value,
"name": database_name,
- "path": database_name
+ "path": database_path,
}
_add_data_table_entry(data_manager_dict, data_table_entry)
diff -r 0c4e821c704b -r 7233538ef3cb data_manager_conf.xml
--- a/data_manager_conf.xml Tue Mar 05 13:11:02 2019 -0500
+++ b/data_manager_conf.xml Tue Mar 05 15:10:42 2019 -0500
@@ -47,4 +47,20 @@
+
+
+
+
+