# HG changeset patch
# User scottx611x
# Date 1466710706 14400
# Node ID 2f03bb5788e1f6117c2bef5372b734b7b2bc5ccf
# Parent  689075526eb3b2943de705a7497b8d7cc4207d25
planemo upload

diff -r 689075526eb3 -r 2f03bb5788e1 data_manager_gene_annotation/data_manager/data_manager.py
--- 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
             }
         }
     }