Mercurial > repos > dfornika > data_manager_build_mob_suite_database
changeset 12:330ca21dddd9 draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_mob_suite_database/ commit ded3b42d8a746eac2973cc17826160e43ac11186-dirty
| author | dfornika |
|---|---|
| date | Mon, 24 Jun 2019 13:23:15 -0400 |
| parents | 4aaf84577a7b |
| children | ca615c36f488 |
| files | data_manager/mob_suite_build_database.py data_manager/mob_suite_build_database.xml |
| diffstat | 2 files changed, 19 insertions(+), 2 deletions(-) [+] |
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--- 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": {
--- 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 @@ <description>database builder</description> <requirements> <requirement type="package" version="1.4.9.1">mob_suite</requirement> + <requirement type="package" version="2.3.0">blast</requirement> + <requirement type="package" version="2.1.1">mash</requirement> </requirements> <version_command>echo '1.4.9.1'</version_command> <command detect_errors="exit_code">