diff --git a/scripts/functional_tests.py b/scripts/functional_tests.py
index 049674067e3..b5823dbe796 100644
--- a/scripts/functional_tests.py
+++ b/scripts/functional_tests.py
@@ -72,6 +72,24 @@ installed_tool_panel_configs = [ 'shed_tool_conf.xml' ]
 # should this serve static resources (scripts, images, styles, etc.)
 STATIC_ENABLED = True
 
+# Set up a job_conf.xml that explicitly limits jobs to 10 minutes.
+job_conf_xml = '''<?xml version="1.0"?>
+<!-- A test job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -->
+<job_conf>
+    <plugins>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
+    </plugins>
+    <handlers>
+        <handler id="main"/>
+    </handlers>
+    <destinations>
+        <destination id="local" runner="local"/>
+    </destinations>
+    <limits>
+        <limit type="walltime">00:10:00</limit>
+    </limits>
+</job_conf>
+'''
 
 def get_static_settings():
     """Returns dictionary of the settings necessary for a galaxy App
@@ -231,6 +249,11 @@ def main():
     if galaxy_test_tmp_dir is None:
         galaxy_test_tmp_dir = tempfile.mkdtemp()
 
+    galaxy_job_conf_file = os.environ.get( 'GALAXY_TEST_JOB_CONF',
+                                           os.path.join( galaxy_test_tmp_dir, 'test_job_conf.xml' ) )
+    # Generate the job_conf.xml file.
+    file( galaxy_job_conf_file, 'w' ).write( job_conf_xml )
+
     database_auto_migrate = False
 
     galaxy_test_proxy_port = None
diff --git a/test/base/twilltestcase.py b/test/base/twilltestcase.py
index f95592c0d9a..f75ba9f2515 100644
--- a/test/base/twilltestcase.py
+++ b/test/base/twilltestcase.py
@@ -1424,20 +1424,21 @@ class TwillTestCase( unittest.TestCase ):
         """Waits for the tools to finish"""
         return self.wait_for(lambda: self.get_running_datasets(), **kwds)
 
-    def wait_for(self, func, maxseconds=120):
+    def wait_for( self, func, **kwd ):
         sleep_amount = 0.1
         slept = 0
-        while slept <= maxseconds:
+        walltime_exceeded = 86400
+        while slept <= walltime_exceeded:
             result = func()
             if result:
                 time.sleep( sleep_amount )
                 slept += sleep_amount
                 sleep_amount *= 2
-                if slept + sleep_amount > maxseconds:
-                    sleep_amount = maxseconds - slept  # don't overshoot maxseconds
+                if slept + sleep_amount > walltime_exceeded:
+                    sleep_amount = walltime_exceeded - slept  # don't overshoot maxseconds
             else:
                 break
-        assert slept < maxseconds
+        assert slept < walltime_exceeded, 'Tool run exceeded reasonable walltime of 24 hours, terminating.'
 
     # Dataset Security stuff
     # Tests associated with users
diff --git a/test/install_and_test_tool_shed_repositories/functional_tests.py b/test/install_and_test_tool_shed_repositories/functional_tests.py
index 669b1b95038..149b56eb6b0 100644
--- a/test/install_and_test_tool_shed_repositories/functional_tests.py
+++ b/test/install_and_test_tool_shed_repositories/functional_tests.py
@@ -91,6 +91,7 @@ else:
 # Should this serve static resources (scripts, images, styles, etc.)?
 STATIC_ENABLED = True
 
+# Set up a job_conf.xml that explicitly limits jobs to 10 minutes.
 job_conf_xml = '''<?xml version="1.0"?>
 <!-- A test job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -->
 <job_conf>