Mercurial > repos > dfornika > data_manager_mash_sketch_builder

changeset 14:b2567cecc145 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 05fb8d8428ce9bc84837bb4043018ab2135f5727-dirty"
author dfornika
date Mon, 24 Feb 2020 19:03:21 +0000
parents 518a9da1be25
children 7941896a92e5
files data_manager/mash_sketch_builder.py
diffstat 1 files changed, 3 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/mash_sketch_builder.py	Mon Feb 24 18:55:39 2020 +0000
+++ b/data_manager/mash_sketch_builder.py	Mon Feb 24 19:03:21 2020 +0000
@@ -18,7 +18,7 @@
 
     os.mkdir(os.path.join(target_directory, UUID))
 
-    sketch_path = os.path.join(UUID, "sketch")
+    sketch_path = os.path.join(target_directory, UUID, "sketch")
 
     args = [
         '-k', str(mash_sketch_args["kmer_size"]),
@@ -27,13 +27,8 @@
         '-p', str(mash_sketch_args["threads"]),
         str(mash_sketch_args["fasta"]),
     ]
-
-    cmd = ' '.join(['mash', 'sketch'] + args)
-
-    pprint(cmd)
     
-    subprocess.check_call(cmd, cwd=target_directory)
-
+    subprocess.check_call(['mash', 'sketch'] + args, cwd=target_directory)
 
     data_table_entry = {
         'data_tables': {
@@ -41,7 +36,7 @@
                 {
                     "value": UUID,
                     "name": sketch_name,
-                    "path": sketch_path,
+                    "path": os.path.join(UUID, 'sketch.msh'),
                 }
             ]
         }