diff --git a/setup.cfg b/setup.cfg
index b73b6ec5ade1..62ef47ece00d 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -7,7 +7,7 @@
 # 501 is line length
 # W503 is line breaks before binary operators, which has been reversed in PEP 8.
 # D** are docstring linting - which we mostly ignore except D302. (Hopefully we will solve more over time).
-ignore = E128,E201,E202,E203,E501,E402,W503,D100,D101,D102,D103,D104,D105,D200,D201,D202,D204,D205,D206,D207,D208,D209,D210,D211,D300,D301,D400,D401,D402,D403
+ignore = E128,E201,E202,E203,E501,E402,W503,D100,D101,D102,D103,D104,D105,D200,D201,D202,D204,D205,D206,D207,D208,D209,D210,D211,D300,D301,D400,D401,D402,D403,D412,D413
 exclude = lib/galaxy/util/jstree.py
 # For flake8-import-order
 # https://github.com/PyCQA/flake8-import-order/blob/master/tests/test_cases/complete_smarkets.py
diff --git a/tox.ini b/tox.ini
index 3e2b84370af9..7a6bb49d9b13 100644
--- a/tox.ini
+++ b/tox.ini
@@ -7,7 +7,7 @@ commands = bash .ci/flake8_wrapper.sh
 whitelist_externals = bash
 deps =
     flake8==3.2.1
-    flake8-docstrings==1.0.3
+    flake8-docstrings==1.1.0
 
 [testenv:py33-lint]
 commands = bash .ci/flake8_py3_wrapper.sh
@@ -86,5 +86,5 @@ commands = bash .ci/flake8_wrapper_docstrings.sh --include
 whitelist_externals = bash
 skip_install = True
 deps =
-    flake8
-    flake8-docstrings==1.0.3
+    flake8==3.2.1
+    flake8-docstrings==1.1.0