diff --git a/lib/galaxy/model/orm/scripts.py b/lib/galaxy/model/orm/scripts.py
index 1b4e8c14836..fc7b4742c97 100644
--- a/lib/galaxy/model/orm/scripts.py
+++ b/lib/galaxy/model/orm/scripts.py
@@ -21,6 +21,12 @@ DATABASE = {
             'default_sqlite_file': './database/universe.sqlite',
             'config_override': 'GALAXY_CONFIG_',
         },
+    "tools":
+        {
+            'repo': 'lib/tool_shed/galaxy_install/migrate',
+            'default_sqlite_file': './database/universe.sqlite',
+            'config_override': 'GALAXY_CONFIG_',
+        },
     "tool_shed":
         {
             'repo': 'lib/galaxy/webapps/tool_shed/model/migrate',
diff --git a/lib/tool_shed/galaxy_install/migrate/check.py b/lib/tool_shed/galaxy_install/migrate/check.py
index c95a0d5e3f7..19ea3705d18 100644
--- a/lib/tool_shed/galaxy_install/migrate/check.py
+++ b/lib/tool_shed/galaxy_install/migrate/check.py
@@ -55,11 +55,10 @@ def verify_tools(app, url, galaxy_config_file=None, engine_options={}):
         if not app.config.running_functional_tests:
             if tool_shed_accessible:
                 # Automatically update the value of the migrate_tools.version database table column.
-                config_arg = ''
+                cmd = ['sh', 'manage_db.sh', 'upgrade', 'tools']
                 if galaxy_config_file:
-                    config_arg = " -c %s" % galaxy_config_file
-                cmd = 'sh manage_tools.sh%s upgrade' % config_arg
-                proc = subprocess.Popen(args=cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+                    cmd[2:2] = ['-c', galaxy_config_file]
+                proc = subprocess.Popen(args=cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
                 return_code = proc.wait()
                 output = proc.stdout.read(32768)
                 if return_code != 0:
diff --git a/manage_tools.sh b/manage_tools.sh
deleted file mode 100644
index 234d1d85fd5..00000000000
--- a/manage_tools.sh
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/bin/sh
-
-cd `dirname $0`
-: ${GALAXY_VIRTUAL_ENV:=.venv}
-
-if [ -d "$GALAXY_VIRTUAL_ENV" ];
-then
-    printf "Activating virtualenv at $GALAXY_VIRTUAL_ENV\n"
-    . "$GALAXY_VIRTUAL_ENV/bin/activate"
-fi
-
-python ./scripts/manage_tools.py $@
diff --git a/scripts/manage_tools.py b/scripts/manage_tools.py
deleted file mode 100644
index fafc9c6e2be..00000000000
--- a/scripts/manage_tools.py
+++ /dev/null
@@ -1,39 +0,0 @@
-from __future__ import print_function
-
-import logging
-import os.path
-import sys
-from ConfigParser import SafeConfigParser
-
-from migrate.versioning.shell import main
-
-sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
-
-from galaxy.model.orm.scripts import read_config_file_arg
-from galaxy.util.properties import load_app_properties
-
-log = logging.getLogger(__name__)
-
-config_file = read_config_file_arg(sys.argv, 'config/galaxy.ini', 'universe_wsgi.ini')
-if not os.path.exists(config_file):
-    print("Galaxy config file does not exist (hint: use '-c config.ini' for non-standard locations): %s" % config_file)
-    sys.exit(1)
-repo = 'lib/tool_shed/galaxy_install/migrate'
-
-properties = load_app_properties(config_file=config_file)
-cp = SafeConfigParser()
-cp.read(config_file)
-
-if config_file == 'config/galaxy.ini.sample' and 'GALAXY_TEST_DBURI' in os.environ:
-    # Running functional tests.
-    db_url = os.environ['GALAXY_TEST_DBURI']
-elif "install_database_connection" in properties:
-    db_url = properties["install_database_connection"]
-elif "database_connection" in properties:
-    db_url = properties["database_connection"]
-elif "database_file" in properties:
-    db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % properties["database_file"]
-else:
-    db_url = "sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE"
-
-main(repository=repo, url=db_url)