diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt
index 40b413679cb..43e16dcec51 100644
--- a/lib/galaxy/dependencies/dev-requirements.txt
+++ b/lib/galaxy/dependencies/dev-requirements.txt
@@ -12,7 +12,7 @@ axe-selenium-python==2.1.6 ; python_version >= "3.7" and python_version < "3.12"
 babel==2.12.1 ; python_version >= "3.7" and python_version < "3.12"
 billiard==3.6.4.0 ; python_version >= "3.7" and python_version < "3.12"
 black==23.3.0 ; python_version >= "3.7" and python_version < "3.12"
-cachecontrol[filecache]==0.12.11 ; python_version >= "3.7" and python_version < "3.12"
+cachecontrol[filecache]==0.13.0 ; python_version >= "3.7" and python_version < "3.12"
 cached-property==1.5.2 ; python_version >= "3.7" and python_version < "3.8"
 celery==5.2.7 ; python_version >= "3.7" and python_version < "3.12"
 certifi==2023.5.7 ; python_version >= "3.7" and python_version < "3.12"
@@ -25,7 +25,7 @@ click==8.1.3 ; python_version >= "3.7" and python_version < "3.12"
 codespell==2.2.4 ; python_version >= "3.7" and python_version < "3.12"
 colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.12" and (sys_platform == "win32" or platform_system == "Windows")
 coverage[toml]==7.2.7 ; python_version >= "3.7" and python_version < "3.12"
-cryptography==40.0.2 ; python_version >= "3.7" and python_version < "3.12"
+cryptography==41.0.1 ; python_version >= "3.7" and python_version < "3.12"
 cwltest==2.3.20230527113600 ; python_version >= "3.7" and python_version < "3.12"
 cycler==0.11.0 ; python_version >= "3.7" and python_version < "3.12"
 darker==1.7.1 ; python_version >= "3.7" and python_version < "3.12"
@@ -33,6 +33,7 @@ defusedxml==0.7.1 ; python_version >= "3.7" and python_version < "3.12"
 deprecated==1.2.14 ; python_version >= "3.7" and python_version < "3.12"
 docutils==0.18.1 ; python_version >= "3.7" and python_version < "3.12"
 exceptiongroup==1.1.1 ; python_version >= "3.7" and python_version < "3.12"
+filelock==3.12.0 ; python_version >= "3.7" and python_version < "3.12"
 fluent-logger==0.10.0 ; python_version >= "3.7" and python_version < "3.12"
 fonttools==4.38.0 ; python_version >= "3.7" and python_version < "3.12"
 frozenlist==1.3.3 ; python_version >= "3.7" and python_version < "3.12"
@@ -50,11 +51,10 @@ jinja2==3.1.2 ; python_version >= "3.7" and python_version < "3.12"
 junit-xml==1.9 ; python_version >= "3.7" and python_version < "3.12"
 kiwisolver==1.4.4 ; python_version >= "3.7" and python_version < "3.12"
 kombu==5.2.4 ; python_version >= "3.7" and python_version < "3.12"
-lockfile==0.12.2 ; python_version >= "3.7" and python_version < "3.12"
 lxml==4.9.2 ; python_version >= "3.7" and python_version < "3.12"
 markdown-it-py==2.2.0 ; python_version >= "3.7" and python_version < "3.12"
 markdown-it-reporter==0.0.2 ; python_version >= "3.7" and python_version < "3.12"
-markupsafe==2.1.2 ; python_version >= "3.7" and python_version < "3.12"
+markupsafe==2.1.3 ; python_version >= "3.7" and python_version < "3.12"
 matplotlib==3.5.3 ; python_version >= "3.7" and python_version < "3.8"
 matplotlib==3.7.1 ; python_version >= "3.8" and python_version < "3.12"
 mdit-py-plugins==0.3.5 ; python_version >= "3.7" and python_version < "3.12"
@@ -106,7 +106,7 @@ requests==2.31.0 ; python_version >= "3.7" and python_version < "3.12"
 responses==0.23.1 ; python_version >= "3.7" and python_version < "3.12"
 ruamel-yaml-clib==0.2.7 ; platform_python_implementation == "CPython" and python_version < "3.11" and python_version >= "3.7"
 ruamel-yaml==0.17.21 ; python_version >= "3.7" and python_version < "3.12"
-schema-salad==8.4.20230511084951 ; python_version >= "3.7" and python_version < "3.12"
+schema-salad==8.4.20230601112322 ; python_version >= "3.7" and python_version < "3.12"
 scipy==1.7.3 ; python_version >= "3.7" and python_version < "3.8"
 scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.12"
 selenium==4.9.1 ; python_version >= "3.7" and python_version < "3.12"
@@ -136,7 +136,7 @@ tuspy==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
 twill==3.1 ; python_version >= "3.7" and python_version < "3.12"
 typed-ast==1.5.4 ; python_version < "3.8" and implementation_name == "cpython" and python_version >= "3.7"
 types-pyyaml==6.0.12.10 ; python_version >= "3.7" and python_version < "3.12"
-typing-extensions==4.6.2 ; python_version >= "3.7" and python_version < "3.12"
+typing-extensions==4.6.3 ; python_version >= "3.7" and python_version < "3.12"
 urllib3==1.26.16 ; python_version >= "3.7" and python_version < "3.12"
 urllib3[socks]==1.26.16 ; python_version >= "3.7" and python_version < "3.12"
 vine==5.0.0 ; python_version >= "3.7" and python_version < "3.12"
diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt
index 7d142fc5d7f..21697bed5c9 100644
--- a/lib/galaxy/dependencies/pinned-lint-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt
@@ -6,5 +6,5 @@ mccabe==0.7.0
 pycodestyle==2.9.1
 pyflakes==2.5.0
 ruff==0.0.270
-typing_extensions==4.6.2
+typing_extensions==4.6.3
 zipp==3.15.0
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index fd544a73d1c..f4cf8f505f0 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -31,8 +31,7 @@ boltons==23.0.0 ; python_version >= "3.7" and python_version < "3.12"
 boto==2.49.0 ; python_version >= "3.7" and python_version < "3.12"
 botocore==1.27.59 ; python_version >= "3.7" and python_version < "3.12"
 bx-python==0.9.0 ; python_version >= "3.7" and python_version < "3.12"
-cachecontrol==0.12.11 ; python_version >= "3.7" and python_version < "3.12"
-cachecontrol[filecache]==0.12.11 ; python_version >= "3.7" and python_version < "3.12"
+cachecontrol[filecache]==0.13.0 ; python_version >= "3.7" and python_version < "3.12"
 cached-property==1.5.2 ; python_version >= "3.7" and python_version < "3.8"
 celery==5.2.7 ; python_version >= "3.7" and python_version < "3.12"
 certifi==2023.5.7 ; python_version >= "3.7" and python_version < "3.12"
@@ -49,9 +48,9 @@ cloudbridge==3.1.0 ; python_version >= "3.7" and python_version < "3.12"
 colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"
 coloredlogs==15.0.1 ; python_version >= "3.7" and python_version < "3.12"
 conda-package-streaming==0.8.0 ; python_version >= "3.7" and python_version < "3.12"
-cryptography==40.0.2 ; python_version >= "3.7" and python_version < "3.12"
-cwl-upgrader==1.2.7 ; python_version >= "3.7" and python_version < "3.12"
-cwl-utils==0.27 ; python_version >= "3.7" and python_version < "3.12"
+cryptography==41.0.1 ; python_version >= "3.7" and python_version < "3.12"
+cwl-upgrader==1.2.8 ; python_version >= "3.7" and python_version < "3.12"
+cwl-utils==0.28 ; python_version >= "3.7" and python_version < "3.12"
 cwltool==3.1.20221109155812 ; python_version >= "3.7" and python_version < "3.12"
 cython==0.29.35 ; python_version >= "3.7" and python_version < "3.12"
 decorator==5.1.1 ; python_version >= "3.7" and python_version < "3.12"
@@ -67,6 +66,7 @@ email-validator==2.0.0.post2 ; python_version >= "3.7" and python_version < "3.1
 exceptiongroup==1.1.1 ; python_version >= "3.7" and python_version < "3.11"
 fastapi-utils==0.2.1 ; python_version >= "3.7" and python_version < "3.12"
 fastapi==0.95.2 ; python_version >= "3.7" and python_version < "3.12"
+filelock==3.12.0 ; python_version >= "3.7" and python_version < "3.12"
 frozenlist==1.3.3 ; python_version >= "3.7" and python_version < "3.12"
 fs==2.4.16 ; python_version >= "3.7" and python_version < "3.12"
 fsspec==2023.1.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -92,12 +92,11 @@ jsonref==1.1.0 ; python_version >= "3.7" and python_version < "3.12"
 jsonschema==4.17.3 ; python_version >= "3.7" and python_version < "3.12"
 kombu==5.2.4 ; python_version >= "3.7" and python_version < "3.12"
 lagom==2.4.1 ; python_version >= "3.7" and python_version < "3.12"
-lockfile==0.12.2 ; python_version >= "3.7" and python_version < "3.12"
 lxml==4.9.2 ; python_version >= "3.7" and python_version < "3.12"
 mako==1.2.4 ; python_version >= "3.7" and python_version < "3.12"
 markdown-it-py==2.2.0 ; python_version >= "3.7" and python_version < "3.12"
 markdown==3.4.3 ; python_version >= "3.7" and python_version < "3.12"
-markupsafe==2.1.2 ; python_version >= "3.7" and python_version < "3.12"
+markupsafe==2.1.3 ; python_version >= "3.7" and python_version < "3.12"
 mdurl==0.1.2 ; python_version >= "3.7" and python_version < "3.12"
 mercurial==6.4.3 ; python_version >= "3.7" and python_version < "3.12"
 mistune==2.0.5 ; python_version >= "3.7" and python_version < "3.12"
@@ -110,7 +109,7 @@ nodeenv==1.8.0 ; python_version >= "3.7" and python_version < "3.12"
 numpy==1.21.6 ; python_version >= "3.7" and python_version < "3.8"
 numpy==1.24.3 ; python_version >= "3.8" and python_version < "3.12"
 oauthlib==3.2.2 ; python_version >= "3.7" and python_version < "3.12"
-orjson==3.8.14 ; python_version >= "3.7" and python_version < "3.12"
+orjson==3.9.0 ; python_version >= "3.7" and python_version < "3.12"
 oyaml==1.0 ; python_version >= "3.7" and python_version < "3.12"
 packaging==23.1 ; python_version >= "3.7" and python_version < "3.12"
 paramiko==3.2.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -157,14 +156,14 @@ requests-oauthlib==1.3.1 ; python_version >= "3.7" and python_version < "3.12"
 requests-toolbelt==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
 requests-unixsocket==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
 requests==2.31.0 ; python_version >= "3.7" and python_version < "3.12"
-rich==13.3.5 ; python_version >= "3.7" and python_version < "3.12"
+rich==13.4.1 ; python_version >= "3.7" and python_version < "3.12"
 rocrate==0.7.0 ; python_version >= "3.7" and python_version < "3.12"
 routes==2.5.1 ; python_version >= "3.7" and python_version < "3.12"
 rsa==4.9 ; python_version >= "3.7" and python_version < "3.12"
 ruamel-yaml-clib==0.2.7 ; platform_python_implementation == "CPython" and python_version < "3.11" and python_version >= "3.7"
 ruamel-yaml==0.17.21 ; python_version >= "3.7" and python_version < "3.12"
 s3fs==2023.1.0 ; python_version >= "3.7" and python_version < "3.12"
-schema-salad==8.4.20230511084951 ; python_version >= "3.7" and python_version < "3.12"
+schema-salad==8.4.20230601112322 ; python_version >= "3.7" and python_version < "3.12"
 setuptools-scm==5.0.2 ; python_version >= "3.7" and python_version < "3.12"
 setuptools==67.8.0 ; python_version >= "3.7" and python_version < "3.12"
 shellescape==3.8.1 ; python_version >= "3.7" and python_version < "3.12"
@@ -186,7 +185,7 @@ tornado==6.2 ; python_version >= "3.7" and python_version < "3.12"
 tqdm==4.65.0 ; python_version >= "3.7" and python_version < "3.12"
 tuspy==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
 tuswsgi==0.5.5 ; python_version >= "3.7" and python_version < "3.12"
-typing-extensions==4.6.2 ; python_version >= "3.7" and python_version < "3.12"
+typing-extensions==4.6.3 ; python_version >= "3.7" and python_version < "3.12"
 tzlocal==2.1 ; python_version >= "3.7" and python_version < "3.12"
 ubiquerg==0.6.2 ; python_version >= "3.7" and python_version < "3.12"
 urllib3==1.26.16 ; python_version >= "3.7" and python_version < "3.12"
diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
index efe4ac06589..a1f40a4ec41 100644
--- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
@@ -1,5 +1,5 @@
 cffi==1.15.1
-cryptography==40.0.2
+cryptography==41.0.1
 mypy==1.3.0
 mypy-extensions==1.0.0
 pycparser==2.21
@@ -12,11 +12,11 @@ types-contextvars==2.4.7.2
 types-dataclasses==0.6.6
 types-docutils==0.20.0.1
 types-Markdown==3.4.2.9
-types-paramiko==3.0.0.10
+types-paramiko==3.2.0.0
 types-pkg-resources==0.1.3
 types-python-dateutil==2.8.19.13
 types-PyYAML==6.0.12.10
-types-requests==2.31.0.0
+types-requests==2.31.0.1
 types-six==1.16.21.8
 types-urllib3==1.26.25.13
-typing_extensions==4.6.2
+typing_extensions==4.6.3