diff --git a/config/tool_shed_wsgi.ini.sample b/config/tool_shed.ini.sample
similarity index 93%
rename from config/tool_shed_wsgi.ini.sample
rename to config/tool_shed.ini.sample
index f83eed3b8cb..029f437e82a 100644
--- a/config/tool_shed_wsgi.ini.sample
+++ b/config/tool_shed.ini.sample
@@ -105,10 +105,10 @@ use_new_layout = true
 #message_box_class = info
 
 # Serving static files (needed if running standalone)
-static_enabled = True
-static_cache_time = 360
-static_dir = %(here)s/static/
-static_images_dir = %(here)s/static/images
-static_favicon_dir = %(here)s/static/favicon.ico
-static_scripts_dir = %(here)s/static/scripts/
-static_style_dir = %(here)s/static/june_2007_style/blue
+#static_enabled = True
+#static_cache_time = 360
+#static_dir = static/
+#static_images_dir = static/images
+#static_favicon_dir = static/favicon.ico
+#static_scripts_dir = static/scripts/
+#static_style_dir = static/style/blue
diff --git a/install_and_test_tool_shed_repositories.sh b/install_and_test_tool_shed_repositories.sh
index 5ec57807757..26ad28f13eb 100644
--- a/install_and_test_tool_shed_repositories.sh
+++ b/install_and_test_tool_shed_repositories.sh
@@ -33,7 +33,7 @@ if [ -z $GALAXY_INSTALL_TEST_TOOL_SHED_URL ] ; then
 fi
 
 if [ -z "$GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF" ] ; then
-	if grep --quiet $GALAXY_INSTALL_TEST_TOOL_SHED_URL tool_sheds_conf.xml; then
+	if grep --quiet $GALAXY_INSTALL_TEST_TOOL_SHED_URL config/tool_sheds_conf.xml.sample; then
 		echo "Tool sheds configuration tool_sheds_conf.xml ok, proceeding."
 	else
 		echo "ERROR: Tool sheds configuration tool_sheds_conf.xml does not have an entry for $GALAXY_INSTALL_TEST_TOOL_SHED_URL."
diff --git a/lib/galaxy/jobs/handler.py b/lib/galaxy/jobs/handler.py
index 0f49fa19844..74d333a7b31 100644
--- a/lib/galaxy/jobs/handler.py
+++ b/lib/galaxy/jobs/handler.py
@@ -101,19 +101,22 @@ class JobHandlerQueue( object ):
         In case the activation is enforced it will filter out the jobs of inactive users.
         """
         jobs_at_startup = []
+        if self.track_jobs_in_database:
+            in_list = ( model.Job.states.QUEUED,
+                        model.Job.states.RUNNING )
+        else:
+            in_list = ( model.Job.states.NEW,
+                        model.Job.states.QUEUED,
+                        model.Job.states.RUNNING )
         if self.app.config.user_activation_on:
                 jobs_at_startup = self.sa_session.query( model.Job ).enable_eagerloads( False ) \
                                   .outerjoin( model.User ) \
-                                  .filter( ( ( model.Job.state == model.Job.states.NEW ) \
-                                             | ( model.Job.state == model.Job.states.RUNNING ) \
-                                             | ( model.Job.state == model.Job.states.QUEUED ) ) \
+                                  .filter( model.Job.state.in_( in_list ) \
                                            & ( model.Job.handler == self.app.config.server_name ) \
                                            & or_( ( model.Job.user_id == None ), ( model.User.active == True ) ) ).all()
         else:
             jobs_at_startup = self.sa_session.query( model.Job ).enable_eagerloads( False ) \
-                              .filter( ( ( model.Job.state == model.Job.states.NEW ) \
-                                         | ( model.Job.state == model.Job.states.RUNNING ) \
-                                         | ( model.Job.state == model.Job.states.QUEUED ) ) \
+                              .filter( model.Job.state.in_( in_list ) \
                                        & ( model.Job.handler == self.app.config.server_name ) ).all()
 
         for job in jobs_at_startup:
diff --git a/lib/galaxy/model/orm/scripts.py b/lib/galaxy/model/orm/scripts.py
index 1161fb5230a..59f31dcd4c4 100644
--- a/lib/galaxy/model/orm/scripts.py
+++ b/lib/galaxy/model/orm/scripts.py
@@ -31,7 +31,7 @@ DATABASE = {
     "tool_shed":
         {
             'repo':  'lib/galaxy/webapps/tool_shed/model/migrate',
-            'config_file': 'tool_shed_wsgi.ini',
+            'config_file': 'config/tool_shed.ini',
             'default_sqlite_file': './database/community.sqlite',
         },
     "install":
@@ -79,7 +79,7 @@ def get_config( argv, cwd=None ):
     ...     p.add_section('app:main')
     ...     p.set('app:main', property, value)
     ...     with open(os.path.join(config_dir, path), 'w') as f: p.write(f)
-    >>> write_ini('tool_shed_wsgi.ini', 'database_connection', 'sqlite:///pg/testdb1')
+    >>> write_ini('tool_shed.ini', 'database_connection', 'sqlite:///pg/testdb1')
     >>> config = get_config(['manage_db.py', 'tool_shed'], cwd=config_dir)
     >>> config['repo']
     'lib/galaxy/webapps/tool_shed/model/migrate'
diff --git a/lib/galaxy/webapps/tool_shed/app.py b/lib/galaxy/webapps/tool_shed/app.py
index 4cf8636db2e..5b411312db7 100644
--- a/lib/galaxy/webapps/tool_shed/app.py
+++ b/lib/galaxy/webapps/tool_shed/app.py
@@ -20,7 +20,7 @@ class UniverseApplication( object ):
     def __init__( self, **kwd ):
         print >> sys.stderr, "python path is: " + ", ".join( sys.path )
         self.name = "tool_shed"
-        # Read the tool_shed_wsgi.ini configuration file and check for errors.
+        # Read the tool_shed.ini configuration file and check for errors.
         self.config = config.Configuration( **kwd )
         self.config.check()
         config.configure_logging( self.config )
diff --git a/lib/galaxy/webapps/tool_shed/buildapp.py b/lib/galaxy/webapps/tool_shed/buildapp.py
index c2ce0c39b4b..14ab0b0337f 100644
--- a/lib/galaxy/webapps/tool_shed/buildapp.py
+++ b/lib/galaxy/webapps/tool_shed/buildapp.py
@@ -220,11 +220,12 @@ def wrap_in_static( app, global_conf, **local_conf ):
     # Send to dynamic app by default
     urlmap["/"] = app
     # Define static mappings from config
-    urlmap["/static"] = Static( conf.get( "static_dir" ), cache_time )
-    urlmap["/images"] = Static( conf.get( "static_images_dir" ), cache_time )
-    urlmap["/static/scripts"] = Static( conf.get( "static_scripts_dir" ), cache_time )
-    urlmap["/static/style"] = Static( conf.get( "static_style_dir" ), cache_time )
-    urlmap["/favicon.ico"] = Static( conf.get( "static_favicon_dir" ), cache_time )
+    urlmap["/static"] = Static( conf.get( "static_dir", "./static/" ), cache_time )
+    urlmap["/images"] = Static( conf.get( "static_images_dir", "./static/images" ), cache_time )
+    urlmap["/static/scripts"] = Static( conf.get( "static_scripts_dir", "./static/scripts/" ), cache_time )
+    urlmap["/static/style"] = Static( conf.get( "static_style_dir", "./static/style/blue" ), cache_time )
+    urlmap["/favicon.ico"] = Static( conf.get( "static_favicon_dir", "./static/favicon.ico" ), cache_time )
+    urlmap["/robots.txt"] = Static( conf.get( "static_robots_txt", "./static/robots.txt" ), cache_time )
     # URL mapper becomes the root webapp
     return urlmap
 
diff --git a/lib/galaxy/webapps/tool_shed/config.py b/lib/galaxy/webapps/tool_shed/config.py
index 6af36108933..05fc22ebd7d 100644
--- a/lib/galaxy/webapps/tool_shed/config.py
+++ b/lib/galaxy/webapps/tool_shed/config.py
@@ -27,6 +27,10 @@ class Configuration( object ):
     def __init__( self, **kwargs ):
         self.config_dict = kwargs
         self.root = kwargs.get( 'root_dir', '.' )
+
+        # Resolve paths of other config files
+        self.__parse_config_file_options( kwargs )
+
         # Collect the umask and primary gid from the environment
         self.umask = os.umask( 077 ) # get the current umask
         os.umask( self.umask ) # can't get w/o set, so set it back
@@ -41,7 +45,6 @@ class Configuration( object ):
         self.new_file_path = resolve_path( kwargs.get( "new_file_path", "database/tmp" ), self.root )
         self.cookie_path = kwargs.get( "cookie_path", "/" )
         self.enable_quotas = string_as_bool( kwargs.get( 'enable_quotas', False ) )
-        self.datatypes_config = kwargs.get( 'datatypes_config_file', 'datatypes_conf.xml' )
         self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root )
         self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" )
         # Tool stuff
@@ -51,8 +54,6 @@ class Configuration( object ):
         self.tool_path = resolve_path( kwargs.get( "tool_path", "tools" ), self.root )
         self.tool_secret = kwargs.get( "tool_secret", "" )
         self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "shed-tool-data" ), os.getcwd() )
-        self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root )
-        self.shed_tool_data_table_config = resolve_path( kwargs.get( 'shed_tool_data_table_config', 'shed_tool_data_table_conf.xml' ), self.root )
         self.integrated_tool_panel_config = resolve_path( kwargs.get( 'integrated_tool_panel_config', 'integrated_tool_panel.xml' ), self.root )
         self.builds_file_path = resolve_path( kwargs.get( "builds_file_path", os.path.join( self.tool_data_path, 'shared', 'ucsc', 'builds.txt') ), self.root )
         self.len_file_path = resolve_path( kwargs.get( "len_file_path", os.path.join( self.tool_data_path, 'shared','ucsc','chrom') ), self.root )
@@ -136,6 +137,47 @@ class Configuration( object ):
         self.citation_cache_data_dir = resolve_path( kwargs.get( "citation_cache_data_dir", "database/tool_shed_citations/data" ), self.root )
         self.citation_cache_lock_dir = resolve_path( kwargs.get( "citation_cache_lock_dir", "database/tool_shed_citations/locks" ), self.root )
 
+    def __parse_config_file_options( self, kwargs ):
+        defaults = dict(
+            datatypes_config_file = [ 'datatypes_conf.xml', 'config/datatypes_conf.xml', 'config/datatypes_conf.xml.sample' ],
+            shed_tool_data_table_config = [ 'shed_tool_data_table_conf.xml', 'config/shed_tool_data_table_conf.xml' ],
+        )
+
+        listify_defaults = dict(
+            tool_data_table_config_path = [ 'tool_data_table_conf.xml', 'config/tool_data_table_conf.xml', 'config/tool_data_table_conf.xml.sample' ],
+        )
+
+        for var, defaults in defaults.items():
+            if kwargs.get( var, None ) is not None:
+                path = kwargs.get( var )
+            else:
+                for default in defaults:
+                    if os.path.exists( resolve_path( default, self.root ) ):
+                        path = default
+                        break
+                else:
+                    path = defaults[-1]
+            setattr( self, var, resolve_path( path, self.root ) )
+
+        for var, defaults in listify_defaults.items():
+            paths = []
+            if kwargs.get( var, None ) is not None:
+                paths = listify( kwargs.get( var ) )
+            else:
+                for default in defaults:
+                    for path in listify( default ):
+                        if not os.path.exists( resolve_path( path, self.root ) ):
+                            break
+                    else:
+                        paths = listify( default )
+                        break
+                else:
+                    paths = listify( defaults[-1] )
+            setattr( self, var, [ resolve_path( x, self.root ) for x in paths ] )
+
+        # Backwards compatibility for names used in too many places to fix
+        self.datatypes_config = self.datatypes_config_file
+
     def get( self, key, default ):
         return self.config_dict.get( key, default )
 
diff --git a/lib/pulsar/client/__init__.py b/lib/pulsar/client/__init__.py
index 86366d3cf7e..4f84a01bde8 100644
--- a/lib/pulsar/client/__init__.py
+++ b/lib/pulsar/client/__init__.py
@@ -34,7 +34,7 @@ line to ``galaxy.ini``::
     test_tool = pulsar://http://remotehost:8913
 
 Remember this must be added after the ``[galaxy:tool_runners]`` header
-in the ``universe.ini`` file.
+in the ``galaxy.ini`` file.
 
 
 """
diff --git a/lib/pulsar/client/amqp_exchange.py b/lib/pulsar/client/amqp_exchange.py
index fd12ace19c6..20591c2259d 100644
--- a/lib/pulsar/client/amqp_exchange.py
+++ b/lib/pulsar/client/amqp_exchange.py
@@ -85,18 +85,27 @@ class PulsarExchange(object):
                 if heartbeat_thread:
                     heartbeat_thread.join()
                 sleep(DEFAULT_RECONNECT_CONSUMER_WAIT)
+            except BaseException:
+                log.exception("Problem consuming queue, consumer quitting in problematic fashion!")
+                raise
 
     def heartbeat(self, connection):
         log.debug('AMQP heartbeat thread alive')
-        while connection.connected:
-            connection.heartbeat_check()
-            sleep(DEFAULT_HEARTBEAT_WAIT)
+        try:
+            while connection.connected:
+                connection.heartbeat_check()
+                sleep(DEFAULT_HEARTBEAT_WAIT)
+        except BaseException:
+            log.exception("Problem with heartbeat, leaving heartbeat method in problematic state!")
+            raise
         log.debug('AMQP heartbeat thread exiting')
 
     def publish(self, name, payload):
+        key = self.__queue_name(name)
+        log.debug("Begin publishing to key %s" % key)
         with self.connection(self.__url) as connection:
             with pools.producers[connection].acquire() as producer:
-                key = self.__queue_name(name)
+                log.debug("Have producer for publishing to key %s" % key)
                 producer.publish(
                     payload,
                     serializer='json',
@@ -105,6 +114,7 @@ class PulsarExchange(object):
                     routing_key=key,
                     **self.__publish_kwds
                 )
+                log.debug("Published to key %s" % key)
 
     def __publish_errback(self, exc, interval):
         log.error("Connection error while publishing: %r", exc, exc_info=1)
diff --git a/lib/pulsar/client/transport/__init__.py b/lib/pulsar/client/transport/__init__.py
index 1f1925e3c1c..e9d10d3f2c5 100644
--- a/lib/pulsar/client/transport/__init__.py
+++ b/lib/pulsar/client/transport/__init__.py
@@ -23,9 +23,16 @@ def __get_transport_type(transport_type, os_module):
             transport_type = 'curl'
     return transport_type
 
-# TODO: Provide urllib implementation if these unavailable,
-# also explore a requests+poster option.
-from .curl import get_file
-from .curl import post_file
+from .curl import curl_available
+from .requests import requests_multipart_post_available
+if curl_available:
+    from .curl import get_file
+    from .curl import post_file
+elif requests_multipart_post_available:
+    from .requests import get_file
+    from .requests import post_file
+else:
+    from .poster import get_file
+    from .poster import post_file
 
 __all__ = [get_transport, get_file, post_file]
diff --git a/lib/pulsar/client/transport/curl.py b/lib/pulsar/client/transport/curl.py
index 9594c719541..e4d3d36b624 100644
--- a/lib/pulsar/client/transport/curl.py
+++ b/lib/pulsar/client/transport/curl.py
@@ -2,10 +2,11 @@ try:
     from cStringIO import StringIO
 except ImportError:
     from io import StringIO
+curl_available = True
 try:
     from pycurl import Curl
 except ImportError:
-    pass
+    curl_available = False
 from os.path import getsize
 
 
diff --git a/lib/pulsar/client/transport/poster.py b/lib/pulsar/client/transport/poster.py
new file mode 100644
index 00000000000..a79cd8dc57e
--- /dev/null
+++ b/lib/pulsar/client/transport/poster.py
@@ -0,0 +1,56 @@
+from __future__ import absolute_import
+try:
+    from urllib2 import urlopen
+except ImportError:
+    from urllib.request import urlopen
+try:
+    from urllib2 import Request
+except ImportError:
+    from urllib.request import Request
+try:
+    from galaxy import eggs
+    eggs.require("poster")
+except ImportError:
+    pass
+
+try:
+    import poster
+except ImportError:
+    poster = None
+
+POSTER_UNAVAILABLE_MESSAGE = "Pulsar configured to use poster module - but it is unavailable. Please install poster."
+
+import logging
+log = logging.getLogger(__name__)
+
+
+if poster is not None:
+    poster.streaminghttp.register_openers()
+
+
+def post_file(url, path):
+    __ensure_poster()
+    try:
+        datagen, headers = poster.encode.multipart_encode({"file": open(path, "rb")})
+        request = Request(url, datagen, headers)
+        return urlopen(request).read()
+    except:
+        log.exception("problem")
+        raise
+
+
+def get_file(url, path):
+    __ensure_poster()
+    request = Request(url=url)
+    response = urlopen(request)
+    with open(path, 'wb') as output:
+        while True:
+            buffer = response.read(1024)
+            if not buffer:
+                break
+            output.write(buffer)
+
+
+def __ensure_poster():
+    if poster is None:
+        raise ImportError(POSTER_UNAVAILABLE_MESSAGE)
diff --git a/lib/pulsar/client/transport/requests.py b/lib/pulsar/client/transport/requests.py
new file mode 100644
index 00000000000..025015d14ed
--- /dev/null
+++ b/lib/pulsar/client/transport/requests.py
@@ -0,0 +1,50 @@
+from __future__ import absolute_import
+try:
+    from galaxy import eggs
+    eggs.require("requests")
+except ImportError:
+    pass
+
+try:
+    import requests
+except ImportError:
+    requests = None
+requests_multipart_post_available = False
+try:
+    import requests_toolbelt
+    requests_multipart_post_available = True
+except ImportError:
+    requests_toolbelt = None
+
+
+REQUESTS_UNAVAILABLE_MESSAGE = "Pulsar configured to use requests module - but it is unavailable. Please install requests."
+REQUESTS_TOOLBELT_UNAVAILABLE_MESSAGE = "Pulsar configured to use requests_toolbelt module - but it is unavailable. Please install requests_toolbelt."
+
+import logging
+log = logging.getLogger(__name__)
+
+
+def post_file(url, path):
+    if requests_toolbelt is None:
+        raise ImportError(REQUESTS_TOOLBELT_UNAVAILABLE_MESSAGE)
+
+    __ensure_requests()
+    m = requests_toolbelt.MultipartEncoder(
+        fields={'file': ('filename', open(path, 'rb'))}
+    )
+    requests.post(url, data=m, headers={'Content-Type': m.content_type})
+
+
+def get_file(url, path):
+    __ensure_requests()
+    r = requests.get(url, stream=True)
+    with open(path, 'wb') as f:
+        for chunk in r.iter_content(chunk_size=1024):
+            if chunk:  # filter out keep-alive new chunks
+                f.write(chunk)
+                f.flush()
+
+
+def __ensure_requests():
+    if requests is None:
+        raise ImportError(REQUESTS_UNAVAILABLE_MESSAGE)
diff --git a/lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh b/lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh
index bdb85bb3a83..279813c7cf6 100755
--- a/lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh
+++ b/lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh
@@ -1,8 +1,10 @@
 #!/bin/bash
 
+: ${TOOL_SHED_CONFIG_FILE:=config/tool_shed.ini.sample}
+
 stop_err() {
 	echo $1
-	python ./scripts/paster.py serve tool_shed_wsgi.ini --pid-file=tool_shed_bootstrap.pid --log-file=tool_shed_bootstrap.log --stop-daemon
+	python ./scripts/paster.py serve ${TOOL_SHED_CONFIG_FILE} --pid-file=tool_shed_bootstrap.pid --log-file=tool_shed_bootstrap.log --stop-daemon
 	exit 1
 }
 
@@ -14,7 +16,7 @@ fi
 
 log_file="lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap.log"
 
-database_result=`python ./lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py --execute check_db --config_file tool_shed_wsgi.ini`
+database_result=`python ./lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py --execute check_db --config_file ${TOOL_SHED_CONFIG_FILE}`
 
 if [ $? -ne 0 ] ; then
 	stop_err "Unable to bootstrap tool shed. $database_result"
@@ -31,8 +33,8 @@ else
 fi
 
 if [ $? -eq 0 ] ; then
-	user_auth=`python ./lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py --execute admin_user_info --config_file tool_shed_wsgi.ini`
-	local_shed_url=`python ./lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py --execute get_url --config_file tool_shed_wsgi.ini`
+	user_auth=`python ./lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py --execute admin_user_info --config_file ${TOOL_SHED_CONFIG_FILE}`
+	local_shed_url=`python ./lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py --execute get_url --config_file ${TOOL_SHED_CONFIG_FILE}`
 fi
 
 admin_user_name=`echo $user_auth | awk 'BEGIN { FS="__SEP__" } ; { print \$1 }'`
@@ -41,18 +43,18 @@ admin_user_password=`echo $user_auth | awk 'BEGIN { FS="__SEP__" } ; { print \$3
 
 echo -n "Creating user '$admin_user_name' with email address '$admin_user_email'..."
 
-python lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py tool_shed_wsgi.ini >> $log_file
+python lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py ${TOOL_SHED_CONFIG_FILE} >> $log_file
 
 echo " done."
 
-sed -i "s/#admin_users = user1@example.org,user2@example.org/admin_users = $admin_user_email/" tool_shed_wsgi.ini
+sed -i "s/#admin_users = user1@example.org,user2@example.org/admin_users = $admin_user_email/" ${TOOL_SHED_CONFIG_FILE}
 echo -n "Starting tool shed in order to populate users and categories... "
 
 if [ -f tool_shed_bootstrap.pid ] ; then
 	stop_err "A bootstrap process is already running."
 fi
 
-python ./scripts/paster.py serve tool_shed_wsgi.ini --pid-file=tool_shed_bootstrap.pid --log-file=tool_shed_bootstrap.log --daemon > /dev/null
+python ./scripts/paster.py serve ${TOOL_SHED_CONFIG_FILE} --pid-file=tool_shed_bootstrap.pid --log-file=tool_shed_bootstrap.log --daemon > /dev/null
 
 shed_pid=`cat tool_shed_bootstrap.pid`
 
@@ -94,6 +96,6 @@ else
 fi
 
 echo "Bootstrap complete, shutting down temporary tool shed process. A log has been saved to tool_shed_bootstrap.log"
-python ./scripts/paster.py serve tool_shed_wsgi.ini --pid-file=tool_shed_bootstrap.pid --log-file=tool_shed_bootstrap.log --stop-daemon
+python ./scripts/paster.py serve ${TOOL_SHED_CONFIG_FILE} --pid-file=tool_shed_bootstrap.pid --log-file=tool_shed_bootstrap.log --stop-daemon
 
-exit 0
\ No newline at end of file
+exit 0
diff --git a/lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py b/lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py
index 4ca3f4387f6..d4f58307290 100755
--- a/lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py
+++ b/lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py
@@ -25,7 +25,7 @@ def check_db( config_parser ):
         db_file = config_parser.get( 'app:main', 'database_file' )
         dburi = "sqlite:///%s?isolation_level=IMMEDIATE" % db_file
     else:
-        print 'The database configuration setting is missing from the tool_shed_wsgi.ini file.  Add this setting before attempting to bootstrap.'
+        print 'The database configuration setting is missing from the tool_shed.ini file.  Add this setting before attempting to bootstrap.'
         exit(1)
     
     sa_session = None
@@ -122,7 +122,7 @@ def main( args ):
         return 1
     
 parser = argparse.ArgumentParser()
-parser.add_argument( '-c', '--config_file', dest='config', action='store', default='tool_shed_wsgi.ini' )
+parser.add_argument( '-c', '--config_file', dest='config', action='store', default='config/tool_shed.ini.sample' )
 parser.add_argument( '-e', '--execute', dest='method', action='store', default='check_db' )
 args = parser.parse_args()
 
diff --git a/run.sh b/run.sh
index b05c5401d09..12b384be6af 100755
--- a/run.sh
+++ b/run.sh
@@ -22,7 +22,7 @@ if [ -z "$GALAXY_CONFIG_FILE" ]; then
     if [ -f universe_wsgi.ini ]; then
         GALAXY_CONFIG_FILE=universe_wsgi.ini
     elif [ -f config/galaxy.ini ]; then
-        GALAXY_CONFIG_FILE=universe_wsgi.ini
+        GALAXY_CONFIG_FILE=config/galaxy.ini
     else
         GALAXY_CONFIG_FILE=config/galaxy.ini.sample
     fi
diff --git a/run_tool_shed.sh b/run_tool_shed.sh
index 1d09ad98449..9f6a0b3eaed 100755
--- a/run_tool_shed.sh
+++ b/run_tool_shed.sh
@@ -12,4 +12,15 @@ if [ $? -eq 0 ] ; then
 	args=`echo $@ | sed "s#-\?-bootstrap_from_tool_shed $tool_shed##"`
 fi
 
-python ./scripts/paster.py serve tool_shed_wsgi.ini --pid-file=tool_shed_webapp.pid --log-file=tool_shed_webapp.log $args
+if [ -z "$TOOL_SHED_CONFIG_FILE" ]; then
+    if [ -f tool_shed_wsgi.ini ]; then
+        TOOL_SHED_CONFIG_FILE=tool_shed_wsgi.ini
+    elif [ -f config/tool_shed.ini ]; then
+        TOOL_SHED_CONFIG_FILE=config/tool_shed.ini
+    else
+        TOOL_SHED_CONFIG_FILE=config/tool_shed.ini.sample
+    fi
+    export TOOL_SHED_CONFIG_FILE
+fi
+
+python ./scripts/paster.py serve $TOOL_SHED_CONFIG_FILE --pid-file=tool_shed_webapp.pid --log-file=tool_shed_webapp.log $args
diff --git a/test/api/test_libraries.py b/test/api/test_libraries.py
index 6060e35d890..1a3bee28dfa 100644
--- a/test/api/test_libraries.py
+++ b/test/api/test_libraries.py
@@ -43,7 +43,7 @@ class LibrariesApiTestCase( api.ApiTestCase, TestsDatasets ):
         library_dataset = show().json()
         self._assert_has_keys( library_dataset, "peek", "data_type" )
         assert library_dataset[ "peek" ].find("create_test") >= 0
-        assert library_dataset[ "data_type" ] == "txt"
+        assert library_dataset[ "file_ext" ] == "txt", library_dataset[ "file_ext" ]
 
     def _create_folder( self, library ):
         create_data = dict(
diff --git a/test/api/test_workflows.py b/test/api/test_workflows.py
index 75a7594586c..95f616c6afc 100644
--- a/test/api/test_workflows.py
+++ b/test/api/test_workflows.py
@@ -26,9 +26,9 @@ class WorkflowsApiTestCase( api.ApiTestCase ):
         self.dataset_populator = DatasetPopulator( self.galaxy_interactor )
         self.dataset_collection_populator = DatasetCollectionPopulator( self.galaxy_interactor )
 
-    def test_show_invalid_is_404( self ):
-        show_response = self._get( "workflow/%s" % self._random_key() )
-        self._assert_status_code_is( show_response, 404 )
+    def test_show_invalid_key_is_400( self ):
+        show_response = self._get( "workflows/%s" % self._random_key() )
+        self._assert_status_code_is( show_response, 400 )
 
     def test_cannot_show_private_workflow( self ):
         workflow_id = self.workflow_populator.simple_workflow( "test_not_importportable" )
@@ -134,12 +134,12 @@ class WorkflowsApiTestCase( api.ApiTestCase ):
             run_workflow_response = self._post( "workflows", data=workflow_request )
             self._assert_status_code_is( run_workflow_response, 403 )
 
-    def test_404_on_invalid_workflow( self ):
+    def test_400_on_invalid_workflow_id( self ):
         workflow = self.workflow_populator.load_workflow( name="test_for_run_does_not_exist" )
         workflow_request, history_id = self._setup_workflow_run( workflow )
         workflow_request[ "workflow_id" ] = self._random_key()
         run_workflow_response = self._post( "workflows", data=workflow_request )
-        self._assert_status_code_is( run_workflow_response, 404 )
+        self._assert_status_code_is( run_workflow_response, 400 )
 
     def test_cannot_run_against_other_users_history( self ):
         workflow = self.workflow_populator.load_workflow( name="test_for_run_does_not_exist" )
@@ -558,21 +558,6 @@ class WorkflowsApiTestCase( api.ApiTestCase ):
         for step in usage_details[ "steps" ]:
             self._assert_has_keys( step, "workflow_step_id", "order_index", "id" )
 
-    @skip_without_tool( "cat1" )
-    def test_post_job_action( self ):
-        """ Tests both import and execution of post job actions.
-        """
-        workflow = self.workflow_populator.load_workflow( name="test_for_pja_run", add_pja=True )
-        workflow_request, history_id = self._setup_workflow_run( workflow )
-        run_workflow_response = self._post( "workflows", data=workflow_request )
-        self._assert_status_code_is( run_workflow_response, 200 )
-        self.dataset_populator.wait_for_history( history_id, assert_ok=True )
-        time.sleep(.1)  # Give another little bit of time for rename (needed?)
-        contents = self._get( "histories/%s/contents" % history_id ).json()
-        # loading workflow with add_pja=True causes workflow output to be
-        # renamed to 'the_new_name'.
-        assert "the_new_name" in map( lambda hda: hda[ "name" ], contents )
-
     def _invocation_details( self, workflow_id, invocation_id ):
         invocation_details_response = self._get( "workflows/%s/usage/%s" % ( workflow_id, invocation_id ) )
         self._assert_status_code_is( invocation_details_response, 200 )
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index 74113f0c83c..76a074ae9c4 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -22,6 +22,8 @@
   <tool file="multi_data_param.xml" />
   <tool file="special_params.xml" />
   <tool file="validation_default.xml" />
+  <tool file="validation_sanitizer.xml" />
+  <tool file="validation_repeat.xml" />
   <tool file="collection_paired_test.xml" />
   <tool file="collection_nested_test.xml" />
   <tool file="collection_mixed_param.xml" />
diff --git a/test/functional/tools/validation_repeat.xml b/test/functional/tools/validation_repeat.xml
new file mode 100644
index 00000000000..4390b1441df
--- /dev/null
+++ b/test/functional/tools/validation_repeat.xml
@@ -0,0 +1,56 @@
+<tool id="validation_repeat" name="Validation (default)">
+  <command>
+    #for $r in $r1
+    echo "${r.text}" >> out1;
+    #end for
+    #for $r in $r2
+    echo "${r.text}" >> out2;
+    #end for
+  </command>
+  <inputs>
+    <repeat name="r1" label="Repeat 1">
+      <param name="text" type="text" label="text input" />
+    </repeat>
+    <repeat name="r2" label="Repeat 2">
+      <param name="text" type="text" label="text input">
+        <sanitizer>
+          <valid initial="none">
+            <add value="a"/>
+            <add value="b"/>
+            <add value="d"/>
+            <add value="e"/>
+          </valid>
+          <mapping initial="none">
+            <add source="@" target="c"/>
+          </mapping>
+        </sanitizer>
+      </param>
+    </repeat>
+  </inputs>
+  <outputs>
+    <data name="out_file1" from_work_dir="out1" />
+    <data name="out_file2" from_work_dir="out2" />
+  </outputs>
+  <tests>
+    <test>
+      <repeat name="r1">
+        <param name="text" value="&quot; ; echo &quot;moo" />
+      </repeat>
+      <repeat name="r2">
+        <param name="text" value="ab@de" />
+      </repeat>
+      <output name="out_file1">
+         <assert_contents>
+            <has_line line="__dq__ X echo __dq__moo" />
+         </assert_contents>
+      </output>
+      <output name="out_file2">
+         <assert_contents>
+            <has_line line="abcde" />
+         </assert_contents>
+      </output>
+    </test>
+  </tests>
+  <help>
+  </help>
+</tool>
diff --git a/test/functional/tools/validation_sanitizer.xml b/test/functional/tools/validation_sanitizer.xml
new file mode 100644
index 00000000000..e8a47a82108
--- /dev/null
+++ b/test/functional/tools/validation_sanitizer.xml
@@ -0,0 +1,35 @@
+<tool id="validation_sanitizer" name="Validation (simple sanitizer)">
+  <command>
+    echo "${text}" >> out1;
+  </command>
+  <inputs>
+    <param name="text" type="text" label="text input">
+      <sanitizer>
+        <valid initial="none">
+          <add value="a"/>
+          <add value="b"/>
+          <add value="d"/>
+          <add value="e"/>
+        </valid>
+        <mapping initial="none">
+          <add source="@" target="c"/>
+        </mapping>
+      </sanitizer>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out_file1" from_work_dir="out1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="text" value="ab@de" />
+      <output name="out_file1">
+         <assert_contents>
+            <has_line line="abcde" />
+         </assert_contents>
+      </output>
+    </test>
+  </tests>
+  <help>
+  </help>
+</tool>