diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt
index b91def0178b..4eb1b2c89a6 100644
--- a/lib/galaxy/dependencies/dev-requirements.txt
+++ b/lib/galaxy/dependencies/dev-requirements.txt
@@ -27,7 +27,7 @@ botocore==1.19.63
 bx-python==0.8.11; python_version >= "3.6"
 cachecontrol==0.11.7; python_version >= "3.6" and python_version < "4"
 cached-property==1.5.2; python_version < "3.8" and python_version >= "3.6"
-cachetools==4.2.1; python_version >= "3.5" and python_version < "4.0" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0")
+cachetools==4.2.2; python_version >= "3.5" and python_version < "4.0" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0")
 celery==5.0.5; python_version >= "3.6"
 certifi==2020.12.5; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" and python_version >= "3.6"
 cffi==1.14.5; implementation_name == "pypy" and python_version >= "3.6" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0")
@@ -57,7 +57,7 @@ deprecated==1.2.12; python_version >= "3.6" and python_full_version < "3.0.0" or
 deprecation==2.1.0
 dictobj==0.4
 docopt==0.6.2
-docutils==0.17.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
+docutils==0.16; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
 dogpile.cache==1.1.2; python_version >= "3.6"
 ecdsa==0.14.1; python_version >= "2.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0"
 fabric3==1.14.post1
@@ -156,7 +156,7 @@ pyfaidx==0.5.9.5
 pygithub==1.55; python_version >= "3.6"
 pygments==2.8.1; python_version >= "3.5"
 pyinotify==0.9.6; sys_platform != "win32" and sys_platform != "darwin" and sys_platform != "sunos5" and python_version >= "3.6"
-pyjwt==2.0.1; python_version >= "3.6"
+pyjwt==2.1.0; python_version >= "3.6"
 pykwalify==1.8.0
 pynacl==1.4.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
 pyparsing==2.4.7; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0")
@@ -196,7 +196,7 @@ requests-oauthlib==1.3.0; python_version >= "2.7" and python_full_version < "3.0
 requests-toolbelt==0.9.1; python_version >= "3.6"
 requests==2.25.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
 requestsexceptions==1.4.0; python_version >= "3.6"
-responses==0.13.2; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
+responses==0.13.3; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
 rfc3986==1.4.0; python_version >= "3.6"
 routes==2.5.1
 rsa==4.7.2; python_version >= "3.5" and python_version < "4" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6")
@@ -214,8 +214,8 @@ snowballstemmer==2.1.0; python_version >= "3.5"
 social-auth-core==3.3.0
 sortedcontainers==2.3.0
 sphinx-markdown-tables==0.0.15
-sphinx-rtd-theme==0.5.1
-sphinx==3.5.3; python_version >= "3.5"
+sphinx-rtd-theme==0.5.2
+sphinx==3.5.4; python_version >= "3.5"
 sphinxcontrib-applehelp==1.0.2; python_version >= "3.5"
 sphinxcontrib-devhelp==1.0.2; python_version >= "3.5"
 sphinxcontrib-htmlhelp==1.0.3; python_version >= "3.5"
diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt
index cdb78a88ca2..133fde0cba5 100644
--- a/lib/galaxy/dependencies/pinned-lint-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt
@@ -1,13 +1,13 @@
 attrs==20.3.0
-flake8==3.9.0
+flake8==3.9.1
 flake8-bugbear==21.4.3
 flake8-import-order==0.18.1
-importlib-metadata==3.10.0
+importlib-metadata==4.0.1
 mccabe==0.6.1
 mypy==0.790
 mypy-extensions==0.4.3
 pycodestyle==2.7.0
 pyflakes==2.3.1
-typed-ast==1.4.2
+typed-ast==1.4.3
 typing-extensions==3.7.4.3
 zipp==3.4.1
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index 5eb56eb360f..e4a6769996d 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -25,7 +25,7 @@ botocore==1.19.63
 bx-python==0.8.11; python_version >= "3.6"
 cachecontrol==0.11.7; python_version >= "3.6" and python_version < "4"
 cached-property==1.5.2; python_version < "3.8" and python_version >= "3.6"
-cachetools==4.2.1; python_version >= "3.5" and python_version < "4.0" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0")
+cachetools==4.2.2; python_version >= "3.5" and python_version < "4.0" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0")
 celery==5.0.5; python_version >= "3.6"
 certifi==2020.12.5; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
 cffi==1.14.5; implementation_name == "pypy" and python_version >= "3.6" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0")
@@ -52,7 +52,7 @@ defusedxml==0.7.1; python_version >= "3.0" and python_full_version < "3.0.0" or
 deprecation==2.1.0
 dictobj==0.4
 docopt==0.6.2
-docutils==0.17.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
+docutils==0.16; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
 dogpile.cache==1.1.2; python_version >= "3.6"
 ecdsa==0.14.1; python_version >= "2.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0"
 fabric3==1.14.post1
@@ -137,7 +137,7 @@ pydot==1.4.2; python_version >= "3.6" and python_full_version < "3.0.0" and pyth
 pyeventsystem==0.1.0
 pyfaidx==0.5.9.5
 pyinotify==0.9.6; sys_platform != "win32" and sys_platform != "darwin" and sys_platform != "sunos5" and python_version >= "3.6"
-pyjwt==2.0.1; python_version >= "3.6"
+pyjwt==2.1.0; python_version >= "3.6"
 pykwalify==1.8.0
 pynacl==1.4.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
 pyparsing==2.4.7; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0")
diff --git a/pyproject.toml b/pyproject.toml
index 73c84e30b9f..70b0bf64603 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -33,7 +33,7 @@ contextvars = {version = "*", python = "~3.6"}
 circus = "*"
 cwltool = "==3.0.20201109103151"
 dictobj = "*"
-docutils = "*"
+docutils = "!=0.17, !=0.17.1"
 Fabric3 = "*"
 fastapi = ">=0.63.0"
 fastapi-utils = "*"