Mercurial > repos > iuc > data_manager_humann2_database_downloader
diff data_manager/data_manager_humann2_download.py @ 2:6112a571f012 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit f474a24a52dcda7fb6681869e24f566d28f1e457
author | iuc |
---|---|
date | Fri, 23 Jun 2017 06:00:47 -0400 |
parents | 048593e41359 |
children | 9244804f69a7 |
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--- a/data_manager/data_manager_humann2_download.py Mon Mar 13 12:34:20 2017 -0400 +++ b/data_manager/data_manager_humann2_download.py Fri Jun 23 06:00:47 2017 -0400 @@ -5,6 +5,7 @@ import json import optparse import os +import shutil import subprocess import sys @@ -15,7 +16,7 @@ "uniref50_diamond": "Full UniRef50", "uniref50_ec_filtered_diamond": "EC-filtered UniRef50", "uniref50_GO_filtered_rapsearch2": "GO filtered UniRef50 for rapsearch2", - "uniref90_diamond": "Full UniRef50", + "uniref90_diamond": "Full UniRef90", "uniref90_ec_filtered_diamond": "EC-filtered UniRef90", "DEMO_diamond": "Demo" } @@ -112,13 +113,12 @@ db_target_dir = os.path.join(target_dir, database) build_target_dir = os.path.join(db_target_dir, build) os.makedirs(build_target_dir) - cmd = "humann2_databases --download %s %s %s" % (database, - build, - db_target_dir) + cmd = "humann2_databases --download %s %s %s --update-config no" % ( + database, + build, + db_target_dir) subprocess.check_call(cmd, shell=True) - print(os.listdir(db_target_dir)) - os.rename(os.path.join(db_target_dir, database), build_target_dir) - print(os.listdir(db_target_dir)) + shutil.move(os.path.join(db_target_dir, database), build_target_dir) add_data_table_entry( data_tables, table_name,