diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index b5cacb61b3d..efe28b1165f 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -1100,13 +1100,13 @@ class ConfiguresGalaxyMixin(object):
         self.security = idencoding.IdEncodingHelper(id_secret=self.config.id_secret)
 
     def _configure_tool_shed_registry(self):
-        import tool_shed.tool_shed_registry
+        import galaxy.tool_shed.tool_shed_registry
 
         # Set up the tool sheds registry
         if os.path.isfile(self.config.tool_sheds_config_file):
-            self.tool_shed_registry = tool_shed.tool_shed_registry.Registry(self.config.tool_sheds_config_file)
+            self.tool_shed_registry = galaxy.tool_shed.tool_shed_registry.Registry(self.config.tool_sheds_config_file)
         else:
-            self.tool_shed_registry = tool_shed.tool_shed_registry.Registry()
+            self.tool_shed_registry = galaxy.tool_shed.tool_shed_registry.Registry()
 
     def _configure_models(self, check_migrate_databases=False, check_migrate_tools=False, config_file=None):
         """
diff --git a/lib/galaxy/tool_shed/util/tool_dependency_util.py b/lib/galaxy/tool_shed/util/tool_dependency_util.py
index 4f06673d50d..3800d5fcc03 100644
--- a/lib/galaxy/tool_shed/util/tool_dependency_util.py
+++ b/lib/galaxy/tool_shed/util/tool_dependency_util.py
@@ -5,9 +5,9 @@ import shutil
 from sqlalchemy import and_
 
 from galaxy import util
-from galaxy.web.form_builder import SelectField
 from galaxy.tool_shed.util.hg_util import get_config_from_disk
 from galaxy.util.tool_shed.xml_util import parse_xml
+from galaxy.web.form_builder import SelectField
 
 log = logging.getLogger(__name__)
 
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index bb41de94bfe..8608b0604d4 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -24,8 +24,6 @@ from six import itervalues, string_types
 from six.moves.urllib.parse import unquote_plus
 from webob.compat import cgi_FieldStorage
 
-import tool_shed.util.repository_util as repository_util
-import tool_shed.util.shed_util_common
 from galaxy import (
     exceptions,
     model
@@ -34,6 +32,8 @@ from galaxy.job_execution import output_collect
 from galaxy.managers.jobs import JobSearch
 from galaxy.metadata import get_metadata_compute_strategy
 from galaxy.model.tags import GalaxyTagHandler
+from galaxy.tool_shed.util.repository_util import get_installed_repository
+from galaxy.tool_shed.util.shed_util_common import set_image_paths
 from galaxy.tool_util.deps import (
     CachedDependencyManager,
 )
@@ -102,9 +102,12 @@ from galaxy.util.template import (
     fill_template,
     refactoring_tool,
 )
+from galaxy.util.tool_shed.common_util import (
+    get_tool_shed_repository_url,
+    get_tool_shed_url_from_tool_shed_registry,
+)
 from galaxy.version import VERSION_MAJOR
 from galaxy.work.context import WorkRequestContext
-from tool_shed.util import common_util
 from .execute import (
     execute as execute_job,
     MappingParameters,
@@ -333,7 +336,7 @@ class ToolBox(BaseGalaxyToolBox):
         # Abstract toolbox doesn't have a dependency on the database, so
         # override _get_tool_shed_repository here to provide this information.
 
-        return repository_util.get_installed_repository(
+        return get_installed_repository(
             self.app,
             tool_shed=tool_shed,
             name=name,
@@ -521,12 +524,12 @@ class Tool(Dictifiable):
     def tool_shed_repository(self):
         # If this tool is included in an installed tool shed repository, return it.
         if self.tool_shed:
-            return repository_util.get_installed_repository(self.app,
-                                                            tool_shed=self.tool_shed,
-                                                            name=self.repository_name,
-                                                            owner=self.repository_owner,
-                                                            installed_changeset_revision=self.installed_changeset_revision,
-                                                            from_cache=True)
+            return get_installed_repository(self.app,
+                                            tool_shed=self.tool_shed,
+                                            name=self.repository_name,
+                                            owner=self.repository_owner,
+                                            installed_changeset_revision=self.installed_changeset_revision,
+                                            from_cache=True)
 
     @property
     def produces_collections_with_unknown_structure(self):
@@ -1244,7 +1247,7 @@ class Tool(Dictifiable):
             self.repository_owner = tool_shed_repository.owner
             self.changeset_revision = tool_shed_repository.changeset_revision
             self.installed_changeset_revision = tool_shed_repository.installed_changeset_revision
-            self.sharable_url = common_util.get_tool_shed_repository_url(
+            self.sharable_url = get_tool_shed_repository_url(
                 self.app, self.tool_shed, self.repository_owner, self.repository_name
             )
 
@@ -1281,7 +1284,7 @@ class Tool(Dictifiable):
         if help_text is not None:
             try:
                 if help_text.find('.. image:: ') >= 0 and (self.tool_shed_repository or self.repository_id):
-                    help_text = tool_shed.util.shed_util_common.set_image_paths(
+                    help_text = set_image_paths(
                         self.app, help_text, encoded_repository_id=self.repository_id, tool_shed_repository=self.tool_shed_repository, tool_id=self.old_id, tool_version=self.version
                     )
             except Exception:
@@ -2174,7 +2177,7 @@ class Tool(Dictifiable):
                             message += 'You can re-run the job with this tool version, which is a different version of the original tool. '
                 else:
                     new_tool_shed_url = '%s/%s/' % (tool.sharable_url, tool.changeset_revision)
-                    old_tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(self.app, tool_id.split('/repos/')[0])
+                    old_tool_shed_url = get_tool_shed_url_from_tool_shed_registry(self.app, tool_id.split('/repos/')[0])
                     old_tool_shed_url = '%s/view/%s/%s/' % (old_tool_shed_url, tool.repository_owner, tool.repository_name)
                     message = 'This job was run with <a href=\"%s\" target=\"_blank\">tool id \"%s\"</a>, version "%s", which is not available. ' % (old_tool_shed_url, tool_id, tool_version)
                     if len(tools) > 1:
diff --git a/lib/galaxy/util/tool_shed/common_util.py b/lib/galaxy/util/tool_shed/common_util.py
index 9d29f83c635..24ff6d361cc 100644
--- a/lib/galaxy/util/tool_shed/common_util.py
+++ b/lib/galaxy/util/tool_shed/common_util.py
@@ -15,7 +15,7 @@ log = logging.getLogger(__name__)
 REPOSITORY_OWNER = 'devteam'
 # not valid for installed Galaxy, fix
 MIGRATE_DIR = os.path.abspath(os.path.join(
-    os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, 'tool_shed', 'galaxy_install', 'migrate'))
+    os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, 'galaxy', 'tool_shed', 'galaxy_install', 'migrate'))
 TOOL_MIGRATION_SCRIPTS_DIR = os.path.join(MIGRATE_DIR, 'scripts')
 TOOL_MIGRATION_VERSIONS_DIR = os.path.join(MIGRATE_DIR, 'versions')
 
diff --git a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
index 8fe57f1a3e2..159e77194e2 100644
--- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
@@ -8,7 +8,6 @@ from paste.httpexceptions import (
 )
 from sqlalchemy import and_
 
-import tool_shed.util.shed_util_common as suc
 from galaxy import (
     exceptions,
     util
@@ -16,12 +15,17 @@ from galaxy import (
 from galaxy.tool_shed.galaxy_install.install_manager import InstallRepositoryManager
 from galaxy.tool_shed.galaxy_install.installed_repository_manager import InstalledRepositoryManager
 from galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager
+from galaxy.tool_shed.util.repository_util import (
+    check_for_updates,
+    get_installed_repository,
+    get_installed_tool_shed_repository,
+    get_tool_shed_repository_by_id,
+)
+from galaxy.tool_shed.util.shed_util_common import have_shed_tool_conf_for_install
+from galaxy.tool_shed.util.tool_util import generate_message_for_invalid_tools
 from galaxy.web import expose_api, require_admin, url_for
 from galaxy.webapps.base.controller import BaseAPIController
-from tool_shed.util import (
-    repository_util,
-    tool_util
-)
+
 
 log = logging.getLogger(__name__)
 
@@ -41,7 +45,7 @@ class ToolShedRepositoriesController(BaseAPIController):
 
     def __ensure_can_install_repos(self, trans):
         # Make sure this Galaxy instance is configured with a shed-related tool panel configuration file.
-        if not suc.have_shed_tool_conf_for_install(self.app):
+        if not have_shed_tool_conf_for_install(self.app):
             message = get_message_for_no_shed_tool_config()
             log.debug(message)
             return dict(status='error', error=message)
@@ -238,7 +242,7 @@ class ToolShedRepositoriesController(BaseAPIController):
         """
         if id:
             try:
-                repository = repository_util.get_tool_shed_repository_by_id(self.app, id)
+                repository = get_tool_shed_repository_by_id(self.app, id)
             except ValueError:
                 raise HTTPBadRequest(detail="No repository with id '%s' found" % id)
         else:
@@ -247,11 +251,11 @@ class ToolShedRepositoriesController(BaseAPIController):
                 tsr_arguments = {key: kwd[key] for key in tsr_arguments}
             except KeyError as e:
                 raise HTTPBadRequest(detail="Missing required parameter '%s'" % e.args[0])
-            repository = repository_util.get_installed_repository(app=self.app,
-                                                                  tool_shed=tsr_arguments['tool_shed_url'],
-                                                                  name=tsr_arguments['name'],
-                                                                  owner=tsr_arguments['owner'],
-                                                                  changeset_revision=tsr_arguments['changeset_revision'])
+            repository = get_installed_repository(app=self.app,
+                                                  tool_shed=tsr_arguments['tool_shed_url'],
+                                                  name=tsr_arguments['name'],
+                                                  owner=tsr_arguments['owner'],
+                                                  changeset_revision=tsr_arguments['changeset_revision'])
             if not repository:
                 raise HTTPBadRequest(detail="Repository not found")
         irm = InstalledRepositoryManager(app=self.app)
@@ -292,7 +296,7 @@ class ToolShedRepositoriesController(BaseAPIController):
         :param id: the encoded repository id
         '''
         repository_id = kwd.get('id', None)
-        message, status = repository_util.check_for_updates(self.app, trans.install_model, repository_id)
+        message, status = check_for_updates(self.app, trans.install_model, repository_id)
         return {'status': status, 'message': message}
 
     @expose_api
@@ -305,7 +309,7 @@ class ToolShedRepositoriesController(BaseAPIController):
             successful = []
             for repository_id in repository_ids:
                 try:
-                    repository = repository_util.get_installed_tool_shed_repository(self.app, repository_id)
+                    repository = get_installed_tool_shed_repository(self.app, repository_id)
                     irmm.set_repository(repository)
                     irmm.reset_all_metadata_on_installed_repository()
                     if irmm.invalid_file_tups:
@@ -350,11 +354,11 @@ class ToolShedRepositoriesController(BaseAPIController):
                 irmm.reset_all_metadata_on_installed_repository()
                 irmm_invalid_file_tups = irmm.get_invalid_file_tups()
                 if irmm_invalid_file_tups:
-                    message = tool_util.generate_message_for_invalid_tools(self.app,
-                                                                           irmm_invalid_file_tups,
-                                                                           repository,
-                                                                           None,
-                                                                           as_html=False)
+                    message = generate_message_for_invalid_tools(self.app,
+                                                                 irmm_invalid_file_tups,
+                                                                 repository,
+                                                                 None,
+                                                                 as_html=False)
                     results['unsuccessful_count'] += 1
                 else:
                     message = "Successfully reset metadata on repository %s owned by %s" % \
@@ -378,7 +382,7 @@ class ToolShedRepositoriesController(BaseAPIController):
         :param id: the encoded id of the ToolShedRepository object
         """
         # Example URL: http://localhost:8763/api/tool_shed_repositories/df7a1f0c02a5b08e
-        tool_shed_repository = repository_util.get_tool_shed_repository_by_id(self.app, id)
+        tool_shed_repository = get_tool_shed_repository_by_id(self.app, id)
         if tool_shed_repository is None:
             log.debug("Unable to locate tool_shed_repository record for id %s." % (str(id)))
             return {}
diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py
index 8dd5ad54242..acf0e86403b 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin.py
@@ -16,21 +16,18 @@ from galaxy import (
 from galaxy.actions.admin import AdminActions
 from galaxy.exceptions import ActionInputError, MessageException
 from galaxy.model import tool_shed_install as install_model
+from galaxy.tool_shed.util.repository_util import get_ids_of_tool_shed_repositories_being_installed
 from galaxy.util import (
     nice_size,
     sanitize_text,
     url_get
 )
+from galaxy.util.tool_shed import common_util, encoding_util
 from galaxy.web import url_for
 from galaxy.web.framework.helpers import grids, time_ago
 from galaxy.web.params import QuotaParamParser
 from galaxy.webapps.base import controller
 from galaxy.webapps.base.controller import UsesQuotaMixin
-from tool_shed.util import (
-    common_util,
-    encoding_util,
-    repository_util
-)
 from tool_shed.util.web_util import escape
 
 
@@ -550,7 +547,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
         status = kwd.get('status', 'done')
         settings = {
             'is_repo_installed': trans.install_model.context.query(trans.install_model.ToolShedRepository).first() is not None,
-            'installing_repository_ids': repository_util.get_ids_of_tool_shed_repositories_being_installed(trans.app, as_string=True),
+            'installing_repository_ids': get_ids_of_tool_shed_repositories_being_installed(trans.app, as_string=True),
             'is_tool_shed_installed': bool(trans.app.tool_shed_registry and trans.app.tool_shed_registry.tool_sheds)
         }
         return self._bootstrapped_client(trans, app_name='admin', settings=settings, message=message, status=status)
@@ -886,7 +883,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
         status = util.restore_text(kwd.get('status', 'done'))
         migration_stages_dict = OrderedDict()
         # FIXME: this isn't valid in an installed context
-        migration_scripts_dir = os.path.abspath(os.path.join(trans.app.config.root, 'lib', 'tool_shed', 'galaxy_install', 'migrate', 'versions'))
+        migration_scripts_dir = os.path.abspath(os.path.join(trans.app.config.root, 'lib', 'galaxy', 'tool_shed', 'galaxy_install', 'migrate', 'versions'))
         modules = os.listdir(migration_scripts_dir)
         modules.sort()
         modules.reverse()
@@ -912,7 +909,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
         message = escape(kwd.get('message', ''))
         status = kwd.get('status', 'done')
         is_repo_installed = trans.install_model.context.query(trans.install_model.ToolShedRepository).first() is not None
-        installing_repository_ids = repository_util.get_ids_of_tool_shed_repositories_being_installed(trans.app, as_string=True)
+        installing_repository_ids = get_ids_of_tool_shed_repositories_being_installed(trans.app, as_string=True)
         return trans.fill_template('/webapps/galaxy/admin/center.mako',
                                    is_repo_installed=is_repo_installed,
                                    installing_repository_ids=installing_repository_ids,
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index e3a9ae48564..fcd5298bafd 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -53,7 +53,7 @@ from galaxy.util.bunch import Bunch
 from galaxy.util.json import safe_loads
 from galaxy.util.rules_dsl import RuleSet
 from galaxy.util.template import fill_template
-from tool_shed.util import common_util
+from galaxy.util.tool_shed.common_util import get_tool_shed_url_from_tool_shed_registry
 
 log = logging.getLogger(__name__)
 
@@ -848,7 +848,7 @@ class ToolModule(WorkflowModule):
             if step.tool_id and step.tool_id != module.tool_id:  # This means the exact version of the tool is not installed. We inform the user.
                 old_tool_shed = step.tool_id.split("/repos/")[0]
                 if old_tool_shed not in tool_id:  # Only display the following warning if the tool comes from a different tool shed
-                    old_tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, old_tool_shed)
+                    old_tool_shed_url = get_tool_shed_url_from_tool_shed_registry(trans.app, old_tool_shed)
                     if not old_tool_shed_url:  # a tool from a different tool_shed has been found, but the original tool shed has been deactivated
                         old_tool_shed_url = "http://" + old_tool_shed  # let's just assume it's either http, or a http is forwarded to https.
                     old_url = old_tool_shed_url + "/view/%s/%s/" % (module.tool.repository_owner, module.tool.repository_name)
diff --git a/test/unit/shed_unit/test_fabric_util.py b/test/unit/shed_unit/test_fabric_util.py
index bb18a2b7bf5..2785ca388ad 100644
--- a/test/unit/shed_unit/test_fabric_util.py
+++ b/test/unit/shed_unit/test_fabric_util.py
@@ -1,6 +1,6 @@
 from contextlib import contextmanager
 
-from tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder import EnvFileBuilder
+from galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder import EnvFileBuilder
 
 
 def test_env_file_builder():
diff --git a/test/unit/shed_unit/test_installed_repository_manager.py b/test/unit/shed_unit/test_installed_repository_manager.py
index 78c901aa42b..91cfcbec2f5 100644
--- a/test/unit/shed_unit/test_installed_repository_manager.py
+++ b/test/unit/shed_unit/test_installed_repository_manager.py
@@ -2,14 +2,14 @@ import os
 
 from mock import MagicMock
 
-from tool_shed.galaxy_install.install_manager import InstallRepositoryManager
-from tool_shed.galaxy_install.installed_repository_manager import InstalledRepositoryManager
-from tool_shed.galaxy_install.update_repository_manager import UpdateRepositoryManager
-from tool_shed.util import (
-    common_util,
+from galaxy.tool_shed.galaxy_install.install_manager import InstallRepositoryManager
+from galaxy.tool_shed.galaxy_install.installed_repository_manager import InstalledRepositoryManager
+from galaxy.tool_shed.galaxy_install.update_repository_manager import UpdateRepositoryManager
+from galaxy.tool_shed.util import (
     hg_util,
     repository_util,
 )
+from galaxy.util.tool_shed import common_util
 from ..tools.test_toolbox import (
     BaseToolBoxTestCase,
     DEFAULT_TEST_REPO
diff --git a/test/unit/shed_unit/test_td_common_util.py b/test/unit/shed_unit/test_td_common_util.py
index d9cc771529a..e57c8eb6cd5 100644
--- a/test/unit/shed_unit/test_td_common_util.py
+++ b/test/unit/shed_unit/test_td_common_util.py
@@ -1,9 +1,9 @@
 from contextlib import contextmanager
 from os.path import join
 
+from galaxy.tool_shed.galaxy_install.tool_dependencies.env_manager import EnvManager
+from galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder import EnvFileBuilder
 from galaxy.util import parse_xml_string
-from tool_shed.galaxy_install.tool_dependencies.env_manager import EnvManager
-from tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder import EnvFileBuilder
 
 TEST_DEPENDENCIES_DIR = "/opt/galaxy/dependencies"
 TEST_INSTALL_DIR = "%s/test_install_dir" % TEST_DEPENDENCIES_DIR
diff --git a/test/unit/shed_unit/test_tool_panel_manager.py b/test/unit/shed_unit/test_tool_panel_manager.py
index e8fd74ecfb5..7c36a26f512 100644
--- a/test/unit/shed_unit/test_tool_panel_manager.py
+++ b/test/unit/shed_unit/test_tool_panel_manager.py
@@ -1,7 +1,7 @@
 import os
 
+from galaxy.tool_shed.galaxy_install.tools import tool_panel_manager
 from galaxy.util import parse_xml
-from tool_shed.galaxy_install.tools import tool_panel_manager
 from tool_shed.tools import tool_version_manager
 from ..tools.test_toolbox import (
     BaseToolBoxTestCase,