--- a/data_manager/data_manager_gemini_download.py	Tue Apr 04 18:09:05 2017 -0400
+++ b/data_manager/data_manager_gemini_download.py	Fri Dec 14 12:40:15 2018 -0500
@@ -6,18 +6,51 @@
 import subprocess
 import sys
 
+import yaml
+
 
 def main():
     today = datetime.date.today()
     params = json.loads( open( sys.argv[1] ).read() )
     target_directory = params[ 'output_data' ][0]['extra_files_path']
     os.mkdir( target_directory )
-    cmd = "gemini --annotation-dir %s update --dataonly %s %s" % (target_directory, params['param_dict']['gerp_bp'], params['param_dict']['cadd'] )
-    subprocess.check_call( cmd, shell=True )
+    # The target_directory needs to be specified twice for the following
+    # invocation of gemini.
+    # In essence, the GEMINI_CONFIG environment variable makes gemini store
+    # its yaml configuration file in that directory, while the
+    # --annotation-dir argument makes it write the same path into the yaml
+    # file, which is then used for determining where the actual annotation
+    # files should be stored.
+    gemini_env = os.environ.copy()
+    gemini_env['GEMINI_CONFIG'] = target_directory
+    cmd = "gemini --annotation-dir %s update --dataonly %s %s" % (
+        target_directory,
+        params['param_dict']['gerp_bp'],
+        params['param_dict']['cadd']
+    )
+    subprocess.check_call( cmd, shell=True, env=gemini_env )
+
+    # modify the newly created gemini config file to contain a relative
+    # annotation dir path, which will be interpreted as relative to
+    # the job working directory at runtime by any gemini tool
+    config_file = os.path.join(target_directory, 'gemini-config.yaml')
+    with open(config_file) as fi:
+        config = yaml.load(fi)
+    config['annotation_dir'] = 'gemini/data'
+    with open(config_file, 'w') as fo:
+        yaml.dump(config, fo, allow_unicode=False, default_flow_style=False)
+
     data_manager_dict = {
         'data_tables': {
-            'gemini_databases': [
-                {'value': today.isoformat(), 'dbkey': 'hg19', 'name': 'GEMINI annotations (%s)' % today.isoformat(), 'path': './%s' % today.isoformat() }
+            'gemini_versioned_databases': [
+                {
+                    'value': today.isoformat(),
+                    'dbkey': 'hg19',
+                    'version': params['param_dict']['gemini_db_version'],
+                    'name':
+                        'GEMINI annotations (%s snapshot)' % today.isoformat(),
+                    'path': './%s' % today.isoformat()
+                }
             ]
         }
     }