Mercurial > repos > dfornika > data_manager_build_kraken2_database
changeset 29:65cbfb5e6f65 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit d59f93c41e32c857f9e82a59c0c408cafc10c233-dirty
| author | dfornika |
|---|---|
| date | Fri, 29 Mar 2019 14:32:59 -0400 |
| parents | b400ae4d47cc |
| children | 0aaff8fb824d |
| files | data_manager/kraken2_build_custom.py data_manager/kraken2_build_custom.xml data_manager/kraken2_build_minikraken.py data_manager/kraken2_build_special.py data_manager/kraken2_build_standard.py |
| diffstat | 5 files changed, 30 insertions(+), 64 deletions(-) [+] |
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--- a/data_manager/kraken2_build_custom.py Wed Mar 27 19:54:12 2019 -0400 +++ b/data_manager/kraken2_build_custom.py Fri Mar 29 14:32:59 2019 -0400 @@ -7,13 +7,12 @@ import json import os import subprocess -import sys DATA_TABLE_NAME = "kraken2_databases" -def kraken2_build(data_manager_dict, kraken2_args, database_name, params, target_directory, data_table_name=DATA_TABLE_NAME): +def kraken2_build(data_manager_dict, kraken2_args, database_name, target_directory, data_table_name=DATA_TABLE_NAME): args = [ '--threads', str(kraken2_args["threads"]), @@ -102,12 +101,12 @@ kraken2_build( data_manager_dict, kraken2_args, - params, + args.database_name, target_directory ) # save info to json file - open(args.params, 'wb').write(json.dumps(data_manager_dict)) + open(args.params, 'w').write(json.dumps(data_manager_dict)) if __name__ == "__main__":
--- a/data_manager/kraken2_build_custom.xml Wed Mar 27 19:54:12 2019 -0400 +++ b/data_manager/kraken2_build_custom.xml Fri Mar 29 14:32:59 2019 -0400 @@ -10,7 +10,7 @@ python '$__tool_directory__/kraken2_build_custom.py' '${out_file}' --threads \${GALAXY_SLOTS:-1} - --db ${database_name} + --db '${database_name}' --kmer-len ${kmer_len} --minimizer-len ${minimizer_len} --minimizer-spaces ${minimizer_spaces}
--- a/data_manager/kraken2_build_minikraken.py Wed Mar 27 19:54:12 2019 -0400 +++ b/data_manager/kraken2_build_minikraken.py Fri Mar 29 14:32:59 2019 -0400 @@ -7,21 +7,19 @@ import errno import json import os -import subprocess -import sys +import shutil +import tarfile + +try: + # Python3 + from urllib.request import urlopen +except ImportError: + from urllib2 import urlopen 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") @@ -40,34 +38,21 @@ now + ")" ]) - database_path = database_value - - args = [ - 'https://ccb.jhu.edu/software/kraken2/dl/minikraken2_' + minikraken2_version + '_8GB.tgz' - ] - - subprocess.check_call(['wget'] + args, cwd=target_directory) - - args = [ - '-p', - database_path, - ] - - subprocess.check_call(['mkdir'] + args, cwd=target_directory) - - args = [ - '-xvzf', - 'minikraken2_' + minikraken2_version + '_8GB.tgz', - '-C', - database_path, - ] - - subprocess.check_call(['tar'] + args, cwd=target_directory) + # download the minikraken2 data + src = urlopen( + 'https://ccb.jhu.edu/software/kraken2/dl/minikraken2_%s_8GB.tgz' + % minikraken2_version + ) + with open('tmp_data.tar.gz', 'wb') as dst: + shutil.copyfileobj(src, dst) + # unpack the downloaded archive to the target directory + with tarfile.open('tmp_data.tar.gz', 'r:gz') as fh: + fh.extractall(target_directory) data_table_entry = { "value": database_value, "name": database_name, - "path": database_path, + "path": database_value, } _add_data_table_entry(data_manager_dict, data_table_entry) @@ -108,7 +93,7 @@ target_directory, ) - open(args.data_manager_json, 'wb').write(json.dumps(data_manager_output)) + open(args.data_manager_json, 'w').write(json.dumps(data_manager_output)) if __name__ == "__main__":
--- a/data_manager/kraken2_build_special.py Wed Mar 27 19:54:12 2019 -0400 +++ b/data_manager/kraken2_build_special.py Fri Mar 29 14:32:59 2019 -0400 @@ -8,20 +8,11 @@ import json import os 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): now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ") @@ -60,7 +51,7 @@ '--db', database_path ] - run(['kraken2-build'] + args, target_directory) + subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) args = [ '--threads', str(kraken2_args["threads"]), @@ -68,7 +59,7 @@ '--db', database_path ] - run(['kraken2-build'] + args, target_directory) + subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) data_table_entry = { "value": database_value, @@ -124,7 +115,7 @@ target_directory, ) - open(args.data_manager_json, 'wb').write(json.dumps(data_manager_output)) + open(args.data_manager_json, 'w').write(json.dumps(data_manager_output)) if __name__ == "__main__":
--- a/data_manager/kraken2_build_standard.py Wed Mar 27 19:54:12 2019 -0400 +++ b/data_manager/kraken2_build_standard.py Fri Mar 29 14:32:59 2019 -0400 @@ -8,20 +8,11 @@ import json import os 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): now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ") @@ -53,7 +44,7 @@ '--db', database_path ] - run(['kraken2-build'] + args, target_directory) + subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) args = [ '--threads', str(kraken2_args["threads"]), @@ -61,7 +52,7 @@ '--db', database_path ] - run(['kraken2-build'] + args, target_directory) + subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) data_table_entry = { "value": database_value, @@ -115,7 +106,7 @@ target_directory, ) - open(args.data_manager_json, 'wb').write(json.dumps(data_manager_output)) + open(args.data_manager_json, 'w').write(json.dumps(data_manager_output)) if __name__ == "__main__":