changeset 26:2f03bb5788e1 draft

planemo upload
author scottx611x
date Thu, 23 Jun 2016 15:38:26 -0400
parents 689075526eb3
children 492505471c3f
files data_manager_gene_annotation/data_manager/data_manager.py
diffstat 1 files changed, 4 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager_gene_annotation/data_manager/data_manager.py	Thu Jun 23 15:34:25 2016 -0400
+++ b/data_manager_gene_annotation/data_manager/data_manager.py	Thu Jun 23 15:38:26 2016 -0400
@@ -46,14 +46,13 @@
                              % e)
             os.remove(file_name)
 
-    return os.path.join(os.getcwd(), file_name)
+    return file_name
 
 
 def main(args):
 
     # Attempt to download gene annotation file from given url
-    gene_annotation_file_path = url_download(
-        "http://www.scott-ouellette.com/gene_annotations/chr1-hg19_genes.gtf", args.name)
+    gene_annotation_file_name = url_download(args.url, args.name)
 
     # Update Data Manager JSON and write to file
     data_manager_entry = {
@@ -61,7 +60,8 @@
             'gene_annotation': {
                 'value': str(datetime.datetime.now()),
                 'dbkey': str(args.name),
-                'name': gene_annotation_file_path.split(".")[0]
+                'name': gene_annotation_file_name.split(".")[0],
+                'path': gene_annotation_file_name
             }
         }
     }