# HG changeset patch
# User dfornika
# Date 1557355143 14400
# Node ID 86bc169b0aeb15b181a41facbff7af842162e545
# Parent 2fd3ebc4fcf3f4efa7bacdcba7bc473dd22b753b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 1137710d16538da15bcd87e1ba382e2afc00031f-dirty
diff -r 2fd3ebc4fcf3 -r 86bc169b0aeb data_manager/kraken2_build_custom.py
--- a/data_manager/kraken2_build_custom.py Fri May 03 19:38:34 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,113 +0,0 @@
-#!/usr/bin/env python
-
-from __future__ import print_function
-
-import argparse
-import errno
-import json
-import os
-import subprocess
-
-
-DATA_TABLE_NAME = "kraken2_databases"
-
-
-def kraken2_build(data_manager_dict, kraken2_args, database_name, target_directory, data_table_name=DATA_TABLE_NAME):
-
- args = [
- '--threads', str(kraken2_args["threads"]),
- '--download-taxonomy',
- '--db', database_name
- ]
-
- subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
-
- args = [
- '--threads', str(kraken2_args["threads"]),
- '--add-to-library', kraken2_args["fasta"],
- '--db', database_name
- ]
-
- subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
-
- args = [
- '--threads', str(kraken2_args["threads"]),
- '--build',
- '--kmer-len', str(kraken2_args["kmer_len"]),
- '--minimizer-len', str(kraken2_args["minimizer_len"]),
- '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
- '--db', database_name
- ]
-
- subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
-
- args = [
- '--threads', str(kraken2_args["threads"]),
- '--clean',
- '--db', database_name
- ]
-
- subprocess.check_call(['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_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( '-d', '--db', dest='database_name', help='database name' )
- 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( '-f', '--fasta', dest='fasta', help='fasta' )
- 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())
- 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,
- args.database_name,
- target_directory
- )
-
- # save info to json file
- open(args.params, 'w').write(json.dumps(data_manager_dict))
-
-
-if __name__ == "__main__":
- main()
diff -r 2fd3ebc4fcf3 -r 86bc169b0aeb data_manager/kraken2_build_custom.xml
--- a/data_manager/kraken2_build_custom.xml Fri May 03 19:38:34 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-
-
- database builder
-
- kraken2
-
- kraken2 -version | head -n 1 | awk '{print $NF}'
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- 10.1186/gb-2014-15-3-r46
-
-
diff -r 2fd3ebc4fcf3 -r 86bc169b0aeb data_manager/kraken2_build_database.py
--- a/data_manager/kraken2_build_database.py Fri May 03 19:38:34 2019 -0400
+++ b/data_manager/kraken2_build_database.py Wed May 08 18:39:03 2019 -0400
@@ -50,7 +50,7 @@
return self.value
-def kraken2_build_standard(data_manager_dict, kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME):
+def kraken2_build_standard(kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME):
now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
database_value = "_".join([
@@ -92,15 +92,21 @@
subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
data_table_entry = {
- "value": database_value,
- "name": database_name,
- "path": database_path,
+ 'data_tables': {
+ data_table_name: [
+ {
+ "value": database_value,
+ "name": database_name,
+ "path": database_path,
+ }
+ ]
+ }
}
- _add_data_table_entry(data_manager_dict, data_table_entry)
+ return data_table_entry
-def kraken2_build_minikraken(data_manager_dict, minikraken2_version, target_directory, data_table_name=DATA_TABLE_NAME):
+def kraken2_build_minikraken(minikraken2_version, target_directory, data_table_name=DATA_TABLE_NAME):
now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
@@ -130,15 +136,21 @@
fh.extractall(target_directory)
data_table_entry = {
- "value": database_value,
- "name": database_name,
- "path": database_value,
+ 'data_tables': {
+ data_table_name: [
+ {
+ "value": database_value,
+ "name": database_name,
+ "path": database_value,
+ }
+ ]
+ }
}
- _add_data_table_entry(data_manager_dict, data_table_entry)
+ return data_table_entry
-def kraken2_build_special(data_manager_dict, kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME):
+def kraken2_build_special(kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME):
now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
@@ -187,15 +199,21 @@
subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
data_table_entry = {
- "value": database_value,
- "name": database_name,
- "path": database_path,
+ 'data_tables': {
+ data_table_name: [
+ {
+ "value": database_value,
+ "name": database_name,
+ "path": database_path,
+ }
+ ]
+ }
}
- _add_data_table_entry(data_manager_dict, data_table_entry)
+ return data_table_entry
-def kraken2_build_custom(data_manager_dict, kraken2_args, custom_database_name, target_directory, data_table_name=DATA_TABLE_NAME):
+def kraken2_build_custom(kraken2_args, custom_database_name, target_directory, data_table_name=DATA_TABLE_NAME):
args = [
'--threads', str(kraken2_args["threads"]),
@@ -233,24 +251,23 @@
subprocess.check_call(['kraken2-build'] + args, target_directory)
data_table_entry = {
- "value": custom_database_name,
- "name": custom_database_name,
- "path": custom_database_name
+ 'data_tables': {
+ data_table_name: [
+ {
+ "value": custom_database_name,
+ "name": custom_database_name,
+ "path": custom_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_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
+ return data_table_entry
def main():
parser = argparse.ArgumentParser()
- parser.add_argument('data_manager_json')
+ parser.add_argument('--extra-files-path', dest='extra_files_path', help='')
parser.add_argument('--kmer-len', dest='kmer_len', type=int, default=35, help='kmer length')
parser.add_argument('--minimizer-len', dest='minimizer_len', type=int, default=31, help='minimizer length')
parser.add_argument('--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces')
@@ -259,12 +276,12 @@
parser.add_argument('--minikraken2-version', dest='minikraken2_version', type=Minikraken2Versions, choices=list(Minikraken2Versions), help='MiniKraken2 version (only applies to --database-type minikraken)')
parser.add_argument('--special-database-type', dest='special_database_type', type=SpecialDatabaseTypes, choices=list(SpecialDatabaseTypes), help='type of special database to build (only applies to --database-type special)')
parser.add_argument('--custom-fasta', dest='custom_fasta', help='fasta file for custom database (only applies to --database-type custom)')
- parser.add_argument( '--custom-database-name', dest='custom_database_name', help='Name for custom database (only applies to --database-type custom)' )
+ parser.add_argument('--custom-database-name', dest='custom_database_name', help='Name for custom database (only applies to --database-type custom)')
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']
+ target_directory = args.extra_files_path
try:
os.mkdir( target_directory )
@@ -276,7 +293,6 @@
data_manager_output = {}
- print(args.database_type)
if str(args.database_type) == 'standard':
kraken2_args = {
"kmer_len": args.kmer_len,
@@ -284,14 +300,12 @@
"minimizer_spaces": args.minimizer_spaces,
"threads": args.threads,
}
- kraken2_build_standard(
- data_manager_output,
+ data_manager_output = kraken2_build_standard(
kraken2_args,
target_directory,
)
elif str(args.database_type) == 'minikraken':
- kraken2_build_minikraken(
- data_manager_output,
+ data_manager_output = kraken2_build_minikraken(
str(args.minikraken2_version),
target_directory
)
@@ -303,8 +317,7 @@
"minimizer_spaces": args.minimizer_spaces,
"threads": args.threads,
}
- kraken2_build_special(
- data_manager_output,
+ data_manager_output = kraken2_build_special(
kraken2_args,
target_directory,
)
@@ -316,8 +329,7 @@
"minimizer_spaces": args.minimizer_spaces,
"threads": args.threads,
}
- kraken2_build_custom(
- data_manager_output,
+ data_manager_output = kraken2_build_custom(
kraken2_args,
args.custom_database_name,
target_directory,
diff -r 2fd3ebc4fcf3 -r 86bc169b0aeb data_manager/kraken2_build_database.xml
--- a/data_manager/kraken2_build_database.xml Fri May 03 19:38:34 2019 -0400
+++ b/data_manager/kraken2_build_database.xml Wed May 08 18:39:03 2019 -0400
@@ -15,7 +15,7 @@
-
- database builder
-
- kraken2
-
- kraken2 -version | head -n 1 | awk '{print $NF}'
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- 10.1186/gb-2014-15-3-r46
-
-
diff -r 2fd3ebc4fcf3 -r 86bc169b0aeb data_manager/kraken2_build_special.py
--- a/data_manager/kraken2_build_special.py Fri May 03 19:38:34 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,122 +0,0 @@
-#!/usr/bin/env python
-
-from __future__ import print_function
-
-import argparse
-import datetime
-import errno
-import json
-import os
-import subprocess
-
-
-DATA_TABLE_NAME = "kraken2_databases"
-
-
-def kraken2_build_standard(data_manager_dict, kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME):
-
- now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
-
- special_database_names = {
- "rdp": "RDP",
- "greengenes": "Greengenes",
- "silva": "Silva",
- }
-
- database_value = "_".join([
- now,
- kraken2_args["special"],
- "kmer-len", str(kraken2_args["kmer_len"]),
- "minimizer-len", str(kraken2_args["minimizer_len"]),
- "minimizer-spaces", str(kraken2_args["minimizer_spaces"]),
- ])
-
- database_name = " ".join([
- special_database_names[kraken2_args["special"]],
- "(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"]),
- '--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_path
- ]
-
- subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
-
- args = [
- '--threads', str(kraken2_args["threads"]),
- '--clean',
- '--db', database_path
- ]
-
- subprocess.check_call(['kraken2-build'] + args, cwd=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( '-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
-
- data_manager_output = {}
-
- kraken2_build_standard(
- data_manager_output,
- kraken2_args,
- target_directory,
- )
-
- open(args.data_manager_json, 'w').write(json.dumps(data_manager_output))
-
-
-if __name__ == "__main__":
- main()
diff -r 2fd3ebc4fcf3 -r 86bc169b0aeb data_manager/kraken2_build_special.xml
--- a/data_manager/kraken2_build_special.xml Fri May 03 19:38:34 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,37 +0,0 @@
-
-
- database builder
-
- kraken2
-
- kraken2 -version | head -n 1 | awk '{print $NF}'
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- 10.1186/gb-2014-15-3-r46
-
-
diff -r 2fd3ebc4fcf3 -r 86bc169b0aeb data_manager/kraken2_build_standard.py
--- a/data_manager/kraken2_build_standard.py Fri May 03 19:38:34 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,113 +0,0 @@
-#!/usr/bin/env python
-
-from __future__ import print_function
-
-import argparse
-import datetime
-import errno
-import json
-import os
-import subprocess
-
-
-DATA_TABLE_NAME = "kraken2_databases"
-
-
-def kraken2_build_standard(data_manager_dict, kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME):
- 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"]),
- ])
-
- 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_path
- ]
-
- subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
-
- args = [
- '--threads', str(kraken2_args["threads"]),
- '--clean',
- '--db', database_path
- ]
-
- subprocess.check_call(['kraken2-build'] + args, cwd=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( '-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,
- "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
-
- data_manager_output = {}
-
- kraken2_build_standard(
- data_manager_output,
- kraken2_args,
- target_directory,
- )
-
- open(args.data_manager_json, 'w').write(json.dumps(data_manager_output))
-
-
-if __name__ == "__main__":
- main()
diff -r 2fd3ebc4fcf3 -r 86bc169b0aeb data_manager/kraken2_build_standard.xml
--- a/data_manager/kraken2_build_standard.xml Fri May 03 19:38:34 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
-
-
- database builder
-
- kraken2
-
- kraken2 -version | head -n 1 | awk '{print $NF}'
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- 10.1186/gb-2014-15-3-r46
-
-
diff -r 2fd3ebc4fcf3 -r 86bc169b0aeb data_manager_conf.xml
--- a/data_manager_conf.xml Fri May 03 19:38:34 2019 -0400
+++ b/data_manager_conf.xml Wed May 08 18:39:03 2019 -0400
@@ -1,18 +1,18 @@
-
-
+