From 7ba16d90adaa0c5f2f8cba34025b267356944c5d Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Fri, 4 May 2012 00:12:43 -0500
Subject: [PATCH 1/2] Augment run.sh to search for the optional environment
 variable GALAXY_UNIVERSE_CONFIG_DIR. If this is set, before Galaxy is
 launched the directory specified by the environment variable is searched for
 ini config files. These files are merged into a single configuration
 structure and written back out as universe.ini.

This should allow for a more modular configuration of Galaxy. The
files are merged in lexiographic order and later files can override
properties specified ealier on. If a consistent naming scheme is used
this can be really useful:

As an example, one might specify the files as such:

  000_galaxy_defaults.ini
  000_default_sqlite_config.ini
  100_institution_specific.ini
  500_job_runner.ini
  500_webapp_0.ini
  500_webapp_1.ini
  500_instance_specific.ini
  500_available_postgres.ini
---
 run.sh                           |  4 ++++
 scripts/build_universe_config.py | 26 ++++++++++++++++++++++++++
 2 files changed, 30 insertions(+)
 create mode 100644 scripts/build_universe_config.py

diff --git a/run.sh b/run.sh
index ca14ece28a7..b3baea9fe58 100644
--- a/run.sh
+++ b/run.sh
@@ -33,6 +33,10 @@ 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..15171f36595
--- /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.ini", 'w'))
+
+if __name__ == '__main__':
+    merge()

From 55b451dcf47d36888ff94eb67d0905180633022a Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 24 May 2012 07:47:14 -0500
Subject: [PATCH 2/2] Fix a typo.

---
 scripts/build_universe_config.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/build_universe_config.py b/scripts/build_universe_config.py
index 15171f36595..dc7f8273969 100644
--- a/scripts/build_universe_config.py
+++ b/scripts/build_universe_config.py
@@ -20,7 +20,7 @@ def merge():
     ## TODO: Expand enviroment variables here, that would
     ## also make Galaxy much easier to configure. 
 
-    parser.write(open("universe.ini", 'w'))
+    parser.write(open("universe_wsgi.ini", 'w'))
 
 if __name__ == '__main__':
     merge()