changeset 1:691bcbfd775d draft

"planemo upload commit 3dc5291eccd1fb516be67694c18a27bda5f69f91"

--- a/data_manager/install_packaged_annotation_data.py	Thu Dec 16 18:26:23 2021 +0000
+++ b/data_manager/install_packaged_annotation_data.py	Thu Dec 16 18:50:18 2021 +0000
@@ -90,19 +90,6 @@
 def fetch_data(source_url, target_file):
     final_file, headers = urlretrieve(source_url, target_file)
     
-def install_data(data, target_directory):
-    # TODO: allow multiple FASTA input files
-    fasta_base_name = os.path.split( fasta_filename )[-1]
-    sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name )
-    os.symlink( fasta_filename, sym_linked_fasta_filename )
-    args = ['bowtie2-build', sym_linked_fasta_filename, index_id]
-    proc = subprocess.Popen(args=args, shell=False, cwd=target_directory)
-    return_code = proc.wait()
-    if return_code:
-        print("Error building index.", file=sys.stderr)
-        sys.exit(return_code)
-    return [' '.join(cmd_quote(arg) for arg in args)]
-
 
 def meta_to_dm_records(meta, dbkey=None):
     data_table_rows = []
@@ -116,7 +103,10 @@
                 'data_format': record['format'],
                 'package_id': meta.meta['id'],
                 'package_name': meta.fullname(),
-                'path': ''
+                'path': '{0}/{1}'.format(
+                    meta.meta['volume'],
+                    meta.meta['build']
+                )
             }
         )
     return data_table_rows