Mercurial > repos > bebatut > data_manager_sortmerna_database_downloader

changeset 1:76e849a0a0b7 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sortmerna_database_downloader commit af5cc2acf0e97637c9a28b80455cc87caf13b79c-dirty
author bebatut
date Wed, 31 May 2017 07:01:57 -0400
parents 505260412cb1
children 663d040f8e5c
files data_manager/data_manager_sortmerna_download.py
diffstat 1 files changed, 4 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- 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(