diff --git a/run.sh b/run.sh
index 669dce50036..d2ba7a377eb 100755
--- a/run.sh
+++ b/run.sh
@@ -36,6 +36,10 @@ for sample in $SAMPLES; do
     fi
 done
 
+if [ -n "$GALAXY_UNIVERSE_CONFIG_DIR" ]; then
+    python ./scripts/build_universe_config.py "$GALAXY_UNIVERSE_CONFIG_DIR"
+fi
+
 # explicitly attempt to fetch eggs before running
 FETCH_EGGS=1
 for arg in "$@"; do
diff --git a/scripts/build_universe_config.py b/scripts/build_universe_config.py
new file mode 100644
index 00000000000..dc7f8273969
--- /dev/null
+++ b/scripts/build_universe_config.py
@@ -0,0 +1,26 @@
+from ConfigParser import ConfigParser
+from os import listdir
+from os.path import join
+from re import match
+from sys import argv
+
+
+def merge():
+    "Merges all .ini files in a specified directory into ./universe.ini"
+    if len(argv) < 2:
+        message = "%s: Must specify directory to merge configuration files from." % argv[0]
+        raise Exception(message)
+    conf_directory = argv[1]
+    conf_files = [f for f in listdir(conf_directory) if match(r'.*\.ini', f)]
+    conf_files.sort()
+
+    parser = ConfigParser()
+    for conf_file in conf_files:
+        parser.read([join(conf_directory, conf_file)])
+    ## TODO: Expand enviroment variables here, that would
+    ## also make Galaxy much easier to configure. 
+
+    parser.write(open("universe_wsgi.ini", 'w'))
+
+if __name__ == '__main__':
+    merge()