# HG changeset patch # User dfornika # Date 1561396995 14400 # Node ID 330ca21dddd98b4ce21e9c679577fb3258e3926e # Parent 4aaf84577a7bb153614c82c9172c36926a623cd5 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_mob_suite_database/ commit ded3b42d8a746eac2973cc17826160e43ac11186-dirty diff -r 4aaf84577a7b -r 330ca21dddd9 data_manager/mob_suite_build_database.py --- a/data_manager/mob_suite_build_database.py Fri Jun 21 20:34:02 2019 -0400 +++ b/data_manager/mob_suite_build_database.py Mon Jun 24 13:23:15 2019 -0400 @@ -26,14 +26,29 @@ database_path = database_value - args = [ + mob_cluster_args_list = [ '--num_threads', mob_cluster_args['num_threads'], '--infile', mob_cluster_args['infile'], '--outdir', database_path, '--mode', mob_cluster_args['mode'], ] - subprocess.check_call(['mob_cluster'] + args, cwd=target_directory) + print(json.dumps(mob_cluster_args)) + + subprocess.check_call(['mob_cluster'] + mob_cluster_args_list, cwd=target_directory) + + makeblastdb_args_list = [ + '-in', database_path, + '-dbtype', 'nucl', + ] + + subprocess.check_call(['makeblastdb'] + makeblastdb_args_list, cwd=target_directory) + + mash_sketch_args_list = [ + '-i', database_path, + ] + + subprocess.check_call(['mash', 'sketch'] + mash_sketch_args_list, cwd=target_directory) data_table_entry = { "data_tables": { diff -r 4aaf84577a7b -r 330ca21dddd9 data_manager/mob_suite_build_database.xml --- a/data_manager/mob_suite_build_database.xml Fri Jun 21 20:34:02 2019 -0400 +++ b/data_manager/mob_suite_build_database.xml Mon Jun 24 13:23:15 2019 -0400 @@ -3,6 +3,8 @@ database builder mob_suite + blast + mash echo '1.4.9.1'