diff --git a/.ci/flake8_blacklist.txt b/.ci/flake8_blacklist.txt
index 04ee7d84b7e..996c483dc14 100644
--- a/.ci/flake8_blacklist.txt
+++ b/.ci/flake8_blacklist.txt
@@ -1,4 +1,5 @@
 .venv/
+.tox/
 client/
 database/
 doc/patch.py
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index f288d368298..e05c20b2a64 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -1677,7 +1677,7 @@ class JobWrapper( object ):
             if metadata_tool is not None:
                 # Due to tool shed hacks for migrate and installed tool tests...
                 # see (``setup_shed_tools_for_test`` in test/base/driver_util.py).
-                dependency_shell_commands = metadata_tool.build_dependency_shell_commands(job_directory=self.working_directory)
+                dependency_shell_commands = metadata_tool.build_dependency_shell_commands(job_directory=self.working_directory, metadata=True)
                 if dependency_shell_commands:
                     dependency_shell_commands = "; ".join(dependency_shell_commands)
                     command = "%s; %s" % (dependency_shell_commands, command)
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 18fdd813f66..c4c00b3ef9d 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1252,13 +1252,14 @@ class Tool( object, Dictifiable ):
         visit_input_values( self.inputs, values, validate_inputs )
         return messages
 
-    def build_dependency_shell_commands( self, job_directory=None ):
+    def build_dependency_shell_commands( self, job_directory=None, metadata=False ):
         """Return a list of commands to be run to populate the current environment to include this tools requirements."""
         return self.app.toolbox.dependency_manager.dependency_shell_commands(
             self.requirements,
             installed_tool_dependencies=self.installed_tool_dependencies,
             tool_dir=self.tool_dir,
             job_directory=job_directory,
+            metadata=metadata,
         )
 
     @property
diff --git a/lib/galaxy/tools/deps/resolvers/conda.py b/lib/galaxy/tools/deps/resolvers/conda.py
index 17b7aa601e1..ac6d322e32d 100644
--- a/lib/galaxy/tools/deps/resolvers/conda.py
+++ b/lib/galaxy/tools/deps/resolvers/conda.py
@@ -125,7 +125,12 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
             return INDETERMINATE_DEPENDENCY
 
         # Have installed conda_target and job_directory to send it too.
-        conda_environment = os.path.join(job_directory, "conda-env")
+        # If dependency is for metadata generation, store environment in conda-metadata-env
+        if kwds.get("metadata", False):
+            conda_env = "conda-metadata-env"
+        else:
+            conda_env = "conda-env"
+        conda_environment = os.path.join(job_directory, conda_env)
         env_path, exit_code = build_isolated_environment(
             conda_target,
             path=conda_environment,
diff --git a/lib/galaxy/web/framework/helpers/__init__.py b/lib/galaxy/web/framework/helpers/__init__.py
index 6ca9b41cdcb..962fd3abd52 100644
--- a/lib/galaxy/web/framework/helpers/__init__.py
+++ b/lib/galaxy/web/framework/helpers/__init__.py
@@ -7,7 +7,7 @@ from datetime import datetime, timedelta
 
 from galaxy.util import hash_util
 from galaxy.util import unicodify
-from galaxy.util.json import safe_dumps as dumps  # noqa (used by mako templates)
+from galaxy.util.json import safe_dumps as dumps  # Used by mako templates # noqa: F401
 from webhelpers import date
 from webhelpers.html.tags import stylesheet_link, javascript_link
 
diff --git a/test/base/driver_util.py b/test/base/driver_util.py
index aafd9d289df..88127c4df56 100644
--- a/test/base/driver_util.py
+++ b/test/base/driver_util.py
@@ -442,7 +442,7 @@ def setup_shed_tools_for_test(app, tmpdir, testing_migrated_tools, testing_insta
             tool_configs.remove(relative_migrated_tool_panel_config)
         for installed_tool_panel_config in INSTALLED_TOOL_PANEL_CONFIGS:
             tool_configs.append(installed_tool_panel_config)
-        from galaxy import tools  # noqa, delay import because this brings in so many modules for small tests
+        from galaxy import tools  # delay import because this brings in so many modules for small tests # noqa
         app.toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app)