# HG changeset patch
# User bebatut
# Date 1496228517 14400
# Node ID 76e849a0a0b7749f23bdc91c848d3d3a146ccbb8
# Parent  505260412cb1550bc2def0d767c968ac98bda787
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sortmerna_database_downloader commit af5cc2acf0e97637c9a28b80455cc87caf13b79c-dirty

diff -r 505260412cb1 -r 76e849a0a0b7 data_manager/data_manager_sortmerna_download.py
--- a/data_manager/data_manager_sortmerna_download.py	Wed May 31 06:38:22 2017 -0400
+++ b/data_manager/data_manager_sortmerna_download.py	Wed May 31 07:01:57 2017 -0400
@@ -130,11 +130,10 @@
         # Move file
         os.rename(input_filepath, output_filepath)
         # Index the file with indexdb_rna
-        ref = "%s,%s" %(output_filepath, os.path.splitext(output_filepath)[0])
-        process = subprocess.run(
-            ["indexdb_rna", "--ref", ref],
-            stdout=subprocess.PIPE,
-            stderr=subprocess.PIPE)
+        command = "indexdb_rna --ref %s,%s" % (
+            output_filepath,
+            os.path.splitext(output_filepath)[0])
+        process = subprocess.call(command, shell=True )
         # Add entry in the data table
         db_name = os.path.splitext(filename)[0]
         add_data_table_entry(