# 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'