Mercurial > repos > iuc > data_manager_humann2_database_downloader

diff data_manager/data_manager_humann2_download.py @ 2:6112a571f012 draft

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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
line wrap: on
line diff
--- 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,