diff --git a/lib/galaxy/dependencies/__init__.py b/lib/galaxy/dependencies/__init__.py
index 5d950c3fa16..e7a5869eb16 100644
--- a/lib/galaxy/dependencies/__init__.py
+++ b/lib/galaxy/dependencies/__init__.py
@@ -22,7 +22,7 @@ class ConditionalDependencies( object ):
         self.get_conditional_requirements()
 
     def parse_configs( self ):
-        self.config = load_app_properties( ini_file=self.config_file )
+        self.config = load_app_properties( config_file=self.config_file )
         job_conf_xml = self.config.get(
             "job_config_file",
             join( dirname( self.config_file ), 'job_conf.xml' ) )
diff --git a/lib/galaxy/util/properties.py b/lib/galaxy/util/properties.py
index b5743dc0ef2..26ba8489108 100644
--- a/lib/galaxy/util/properties.py
+++ b/lib/galaxy/util/properties.py
@@ -6,6 +6,8 @@ import os
 import os.path
 import sys
 
+import yaml
+
 from six import iteritems
 from six.moves.configparser import ConfigParser
 
@@ -35,21 +37,29 @@ def find_config_file(default, old_default, explicit, cwd=None):
 def load_app_properties(
     kwds={},
     ini_file=None,
-    ini_section="app:main",
+    ini_section=None,
+    config_file=None,
+    config_section=None,
     config_prefix="GALAXY_CONFIG_"
 ):
     properties = kwds.copy() if kwds else {}
-    if ini_file:
-        defaults = {
-            'here': os.path.dirname(os.path.abspath(ini_file)),
-            '__file__': os.path.abspath(ini_file)
-        }
-        parser = NicerConfigParser(ini_file, defaults=defaults)
-        parser.optionxform = str  # Don't lower-case keys
-        with open(ini_file) as f:
-            parser.read_file(f)
+    if config_file is None:
+        config_file = ini_file
+        config_section = ini_section
 
-        properties.update( dict( parser.items( ini_section ) ) )
+    if config_file:
+        if not config_file.endswith(".yml") and not config_file.endswith(".yml.sample"):
+            if config_section is None:
+                config_section = "app:main"
+            parser = nice_config_parser(config_file)
+            properties.update( dict( parser.items( config_section ) ) )
+        else:
+            if config_section is None:
+                config_section = "galaxy"
+
+            with open(config_file, "r") as f:
+                raw_properties = yaml.load(f)
+            properties = raw_properties[config_section] or {}
 
     override_prefix = "%sOVERRIDE_" % config_prefix
     for key in os.environ:
@@ -64,6 +74,18 @@ def load_app_properties(
     return properties
 
 
+def nice_config_parser(path):
+    defaults = {
+        'here': os.path.dirname(os.path.abspath(path)),
+        '__file__': os.path.abspath(path)
+    }
+    parser = NicerConfigParser(path, defaults=defaults)
+    parser.optionxform = str  # Don't lower-case keys
+    with open(path) as f:
+        parser.read_file(f)
+    return parser
+
+
 class NicerConfigParser(ConfigParser):
 
     def __init__(self, filename, *args, **kw):
diff --git a/lib/galaxy/web/framework/webapp.py b/lib/galaxy/web/framework/webapp.py
index 6e13934c0e6..28bb34ab485 100644
--- a/lib/galaxy/web/framework/webapp.py
+++ b/lib/galaxy/web/framework/webapp.py
@@ -27,6 +27,7 @@ from galaxy.exceptions import MessageException
 from galaxy import util
 from galaxy.util import asbool
 from galaxy.util import safe_str_cmp
+from galaxy.util.postfork import process_is_uwsgi
 from galaxy.util.sanitize_html import sanitize_html
 
 from galaxy.managers import context
@@ -954,6 +955,27 @@ class GalaxyWebTransaction( base.DefaultWebTransaction,
         return str(template)
 
 
+def build_native_uwsgi_app( paste_factory, config_section ):
+    """uwsgi can load paste factories with --ini-paste, but this builds non-paste uwsgi apps.
+
+    In particular these are useful with --yaml or --json for config."""
+    if not process_is_uwsgi:
+        return None
+    else:
+        import uwsgi
+        uwsgi_opt = uwsgi.opt
+        config_file = uwsgi_opt.get("yaml") or uwsgi_opt.get("json")
+        if not config_file:
+            # Probably loaded via --ini-paste - expect paste app.
+            return None
+
+        uwsgi_app = paste_factory(uwsgi.opt, load_app_kwds={
+            "config_file": config_file,
+            "config_section": config_section,
+        })
+        return uwsgi_app
+
+
 def build_url_map( app, global_conf, local_conf ):
     from paste.urlmap import URLMap
     from galaxy.web.framework.middleware.static import CacheableStaticURLParser as Static
diff --git a/lib/galaxy/webapps/tool_shed/buildapp.py b/lib/galaxy/webapps/tool_shed/buildapp.py
index 7090bc4c066..03e71335ad5 100644
--- a/lib/galaxy/webapps/tool_shed/buildapp.py
+++ b/lib/galaxy/webapps/tool_shed/buildapp.py
@@ -309,3 +309,7 @@ def _map_redirects( mapper ):
 
     mapper.redirect( "/repository/status_for_installed_repository", "/api/repositories/updates/", _redirect_code="301 Moved Permanently", conditions=dict( function=forward_qs ) )
     return mapper
+
+
+def uwsgi_app():
+    return galaxy.web.framework.webapp.build_native_uwsgi_app( app_factory, "tool_shed" )
diff --git a/scripts/manage_tools.py b/scripts/manage_tools.py
index 5d17e41347f..66d13f80da9 100644
--- a/scripts/manage_tools.py
+++ b/scripts/manage_tools.py
@@ -18,7 +18,7 @@ if not os.path.exists( config_file ):
     sys.exit( 1 )
 repo = 'lib/tool_shed/galaxy_install/migrate'
 
-properties = load_app_properties( ini_file=config_file )
+properties = load_app_properties( config_file=config_file )
 cp = SafeConfigParser()
 cp.read( config_file )