Mercurial > repos > dfornika > data_manager_build_mob_suite_database

changeset 16:c946718c1328 draft

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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 14:25:41 -0400
parents b2966fea70b0
children 746cfbee7afd
files data_manager/mob_suite_build_database.py
diffstat 1 files changed, 3 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/mob_suite_build_database.py	Mon Jun 24 14:14:45 2019 -0400
+++ b/data_manager/mob_suite_build_database.py	Mon Jun 24 14:25:41 2019 -0400
@@ -7,6 +7,7 @@
 import errno
 import json
 import os
+import shutil
 import string
 import subprocess
 import sys
@@ -34,7 +35,7 @@
         '--mode', mob_cluster_args['mode'],
     ]
 
-    print(json.dumps(mob_cluster_args))
+    print(json.dumps(mob_cluster_args_list))
 
     print("Sleeping for 20s")
     time.sleep(20)
@@ -42,7 +43,7 @@
     
     subprocess.check_call(['mob_cluster'] + mob_cluster_args_list, cwd=target_directory)
 
-    os.rename(
+    shutil.copyfile(
         os.path.join(database_path, 'references_updated.fasta'),
         os.path.join(database_path, 'ncbi_plasmid_full_seqs.fas')
     )