diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt
index 48e90daebfd..9a82f736711 100644
--- a/lib/galaxy/dependencies/dev-requirements.txt
+++ b/lib/galaxy/dependencies/dev-requirements.txt
@@ -12,9 +12,9 @@ babel==2.18.0
 backports-asyncio-runner==1.2.0 ; python_full_version < '3.11'
 backports-tarfile==1.2.0 ; python_full_version < '3.12' and platform_machine != 'ppc64le' and platform_machine != 's390x'
 black==26.3.1
-boto3==1.42.70
-botocore==1.42.70
-build==1.4.2
+boto3==1.42.84
+botocore==1.42.84
+build==1.4.3
 cachecontrol==0.14.4
 cachetools==7.0.5
 cattrs==26.1.0
@@ -47,8 +47,8 @@ frozenlist==1.8.0
 fsspec==2026.3.0
 galaxy-release-util==0.3.2
 gcsfs==2026.3.0
-google-api-core==2.30.2
-google-auth==2.49.1
+google-api-core==2.30.3
+google-auth==2.49.2
 google-auth-oauthlib==1.3.1
 google-cloud-core==2.5.1
 google-cloud-storage==3.10.1
@@ -56,7 +56,7 @@ google-cloud-storage-control==1.11.0
 google-crc32c==1.8.0
 google-resumable-media==2.8.2
 googleapis-common-protos==1.74.0
-greenlet==3.3.2
+greenlet==3.4.0
 grpc-google-iam-v1==0.14.4
 grpcio==1.80.0
 grpcio-status==1.80.0
@@ -84,8 +84,8 @@ jsonschema-specifications==2025.9.1
 junit-xml==1.9
 keyring==25.7.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 kiwisolver==1.5.0
-librt==0.8.1 ; platform_python_implementation != 'PyPy'
-lxml==6.0.2
+librt==0.9.0 ; platform_python_implementation != 'PyPy'
+lxml==6.0.3
 markdown-it-py==3.0.0 ; python_full_version < '3.11'
 markdown-it-py==4.0.0 ; python_full_version >= '3.11'
 markdown-it-reporter==0.0.2
@@ -95,7 +95,7 @@ mdit-py-plugins==0.5.0
 mdurl==0.1.2
 mirakuru==3.0.2
 mistune==3.2.0
-more-itertools==11.0.1 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
+more-itertools==11.0.2 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 msgpack==1.1.2
 multidict==6.7.1
 mypy==1.20.0
@@ -114,7 +114,7 @@ pathspec==1.0.4
 pfzy==0.3.4
 pillow==12.2.0
 pkce==1.0.3
-platformdirs==4.9.4
+platformdirs==4.9.6
 playwright==1.58.0
 pluggy==1.6.0
 port-for==1.0.0
@@ -137,7 +137,7 @@ pyparsing==3.3.2
 pyproject-hooks==1.2.0
 pyshacl==0.31.0
 pysocks==1.7.1
-pytest==9.0.2
+pytest==9.0.3
 pytest-asyncio==1.3.0
 pytest-base-url==2.1.0
 pytest-cov==7.1.0
@@ -177,7 +177,7 @@ schema-salad==8.9.20260327095315
 scipy==1.15.3 ; python_full_version < '3.11'
 scipy==1.17.1 ; python_full_version >= '3.11'
 secretstorage==3.5.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
-selenium==4.41.0
+selenium==4.43.0
 seletools==1.5.0
 six==1.17.0
 sniffio==1.3.1
@@ -208,8 +208,8 @@ trio==0.33.0
 trio-websocket==0.12.2
 tuspy==1.1.0
 twine==6.2.0
-types-cachetools==6.2.0.20260317
-types-requests==2.33.0.20260402
+types-cachetools==6.2.0.20260408
+types-requests==2.33.0.20260408
 typing-extensions==4.15.0
 typos==1.45.0
 tzdata==2026.1 ; sys_platform == 'win32'
diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt
index 2eb242e2c73..fb15e07de1a 100644
--- a/lib/galaxy/dependencies/pinned-lint-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt
@@ -4,4 +4,4 @@ flake8-bugbear==25.11.29
 mccabe==0.7.0
 pycodestyle==2.14.0
 pyflakes==3.4.0
-ruff==0.15.9
+ruff==0.15.10
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index 87880c29c29..4aa9447dc55 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -3,7 +3,7 @@
 a2wsgi==1.10.10
 adal==1.2.7
 ag-ui-protocol==0.1.15
-aiobotocore==3.3.0
+aiobotocore==3.4.0
 aiofile==3.9.0
 aiofiles==25.1.0
 aiohappyeyeballs==2.6.1
@@ -14,7 +14,7 @@ alembic==1.18.4
 amqp==5.3.1
 annotated-doc==0.0.4
 annotated-types==0.7.0
-anthropic==0.89.0
+anthropic==0.94.0
 anyio==4.13.0
 apispec==6.10.0
 appdirs==1.4.4
@@ -36,8 +36,8 @@ bioblend==1.8.0
 bleach==6.3.0
 boltons==25.0.0
 boto==2.49.0
-boto3==1.42.70
-botocore==1.42.70
+boto3==1.42.84
+botocore==1.42.84
 bx-python==0.14.0
 cachecontrol==0.14.4
 cachetools==7.0.5
@@ -53,7 +53,7 @@ click-plugins==1.1.1.2
 click-repl==0.3.0
 cloudauthz==0.6.0
 cloudbridge==3.2.0
-cohere==5.21.1 ; sys_platform != 'emscripten'
+cohere==6.1.0 ; sys_platform != 'emscripten'
 colorama==0.4.6 ; sys_platform == 'win32'
 coloredlogs==15.0.1
 conda-package-streaming==0.12.0
@@ -62,7 +62,7 @@ ct3==3.4.0.post5
 cwl-upgrader==1.2.15
 cwl-utils==0.41
 cwltool==3.1.20260315121657
-cyclopts==4.10.1
+cyclopts==4.10.2
 defusedxml==0.7.1
 deprecated==1.3.1
 deprecation==2.1.0
@@ -82,7 +82,7 @@ exceptiongroup==1.3.1
 executing==2.2.1
 fastapi==0.135.3
 fastavro==1.12.1 ; sys_platform != 'emscripten'
-fastmcp==3.2.0
+fastmcp==3.2.3
 filelock==3.25.2
 fissix==24.4.24
 frozenlist==1.8.0
@@ -90,13 +90,13 @@ fs==2.4.16
 fsspec==2026.3.0
 future==1.0.0
 genai-prices==0.0.56
-google-api-core==2.30.2
-google-auth==2.49.1
+google-api-core==2.30.3
+google-auth==2.49.2
 google-cloud-batch==0.21.0
-google-genai==1.70.0
+google-genai==1.72.0
 googleapis-common-protos==1.74.0
 gravity==1.2.0
-greenlet==3.3.2 ; platform_machine == 'AMD64' or platform_machine == 'WIN32' or platform_machine == 'aarch64' or platform_machine == 'amd64' or platform_machine == 'ppc64le' or platform_machine == 'win32' or platform_machine == 'x86_64'
+greenlet==3.4.0 ; platform_machine == 'AMD64' or platform_machine == 'WIN32' or platform_machine == 'aarch64' or platform_machine == 'amd64' or platform_machine == 'ppc64le' or platform_machine == 'win32' or platform_machine == 'x86_64'
 griffelib==2.0.2
 groq==1.1.2
 grpcio==1.80.0
@@ -110,13 +110,13 @@ hf-xet==1.4.3 ; platform_machine == 'AMD64' or platform_machine == 'aarch64' or
 httpcore==1.0.9
 httpx==0.28.1
 httpx-sse==0.4.3
-huggingface-hub==1.9.0
+huggingface-hub==1.10.1
 humanfriendly==10.0
 idna==3.11
 ijson==3.5.0
 importlib-metadata==8.7.1
 importlib-resources==6.5.2 ; python_full_version < '3.12'
-invoke==2.2.1
+invoke==3.0.3
 isa-rwval==0.10.11
 isal==1.8.0
 isodate==0.7.2 ; python_full_version < '3.11'
@@ -125,7 +125,7 @@ jaraco-context==6.1.2
 jaraco-functools==4.4.0
 jeepney==0.9.0 ; sys_platform == 'linux'
 jinja2==3.1.6
-jiter==0.13.0
+jiter==0.14.0
 jmespath==1.1.0
 jsonpath-python==1.1.5
 jsonref==1.1.0
@@ -137,9 +137,9 @@ kombu==5.6.2
 lagom==2.7.7
 legacy-cgi==2.6.4 ; python_full_version >= '3.13'
 limits==5.8.0
-logfire==4.31.0
-logfire-api==4.31.0
-lxml==6.0.2
+logfire==4.32.0
+logfire-api==4.32.0
+lxml==6.0.3
 mako==1.3.10
 markdown==3.10.2
 markdown-it-py==3.0.0 ; python_full_version < '3.11'
@@ -148,11 +148,11 @@ markupsafe==3.0.3
 mcp==1.27.0
 mdurl==0.1.2
 mercurial==7.2.1
-mistralai==2.3.0
+mistralai==2.3.2
 mistune==3.2.0
-more-itertools==11.0.1
+more-itertools==11.0.2
 mrcfile==1.5.4
-msal==1.35.1
+msal==1.36.0
 msgpack==1.1.2
 multidict==6.7.1
 mypy-extensions==1.1.0
@@ -164,7 +164,7 @@ nodejs-wheel-binaries==22.20.0
 numpy==2.2.6 ; python_full_version < '3.11'
 numpy==2.4.4 ; python_full_version >= '3.11'
 oauthlib==3.3.1
-openai==2.30.0
+openai==2.31.0
 openapi-pydantic==0.5.1
 openpyxl==3.1.5
 opentelemetry-api==1.39.1
@@ -185,7 +185,7 @@ pastedeploy==3.1.0
 pathable==0.5.0
 pebble==5.2.0
 pillow==12.2.0
-platformdirs==4.9.4
+platformdirs==4.9.6
 prompt-toolkit==3.0.52
 propcache==0.4.1
 proto-plus==1.27.2
@@ -199,11 +199,11 @@ pyasn1-modules==0.4.2
 pycparser==3.0 ; (implementation_name != 'PyPy' and platform_python_implementation != 'PyPy') or (implementation_name == 'pypy' and platform_python_implementation == 'PyPy')
 pycryptodome==3.23.0
 pydantic==2.12.5
-pydantic-ai==1.77.0
-pydantic-ai-slim==1.77.0
+pydantic-ai==1.80.0
+pydantic-ai-slim==1.80.0
 pydantic-core==2.41.5
-pydantic-evals==1.77.0
-pydantic-graph==1.77.0
+pydantic-evals==1.80.0
+pydantic-graph==1.80.0
 pydantic-handlebars==0.1.0
 pydantic-settings==2.13.1
 pydantic-tes==0.3.0
@@ -224,7 +224,7 @@ pysam==0.23.3
 python-dateutil==2.9.0.post0
 python-dotenv==1.2.2
 python-magic==0.4.27
-python-multipart==0.0.22
+python-multipart==0.0.26
 python-slugify==8.0.4
 python3-openid==3.2.0
 pytz==2026.1.post1
@@ -267,7 +267,7 @@ starlette==1.0.0
 starlette-context==0.5.1
 supervisor==4.3.0
 svgwrite==1.4.3
-temporalio==1.24.0
+temporalio==1.25.0
 tenacity==9.1.4
 text-unidecode==1.3
 tifffile==2025.5.10 ; python_full_version < '3.11'
@@ -281,16 +281,16 @@ tqdm==4.67.3
 tuspy==1.1.0
 tuspyserver==4.2.3
 typer==0.24.1
-types-protobuf==7.34.1.20260403
-types-requests==2.33.0.20260402 ; sys_platform != 'emscripten'
+types-protobuf==6.32.1.20260221
+types-requests==2.33.0.20260408 ; sys_platform != 'emscripten'
 typing-extensions==4.15.0
 typing-inspection==0.4.2
 tzdata==2026.1
 tzlocal==5.3.1
 ubiquerg==0.9.3
-uncalled-for==0.2.0
+uncalled-for==0.3.1
 urllib3==2.6.3
-uvicorn==0.43.0
+uvicorn==0.44.0
 uvloop==0.22.1
 vine==5.1.0
 watchfiles==1.1.1
diff --git a/lib/galaxy/dependencies/pinned-test-requirements.txt b/lib/galaxy/dependencies/pinned-test-requirements.txt
index b9cb08198a5..8fda4141585 100644
--- a/lib/galaxy/dependencies/pinned-test-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-test-requirements.txt
@@ -8,8 +8,8 @@ async-timeout==5.0.1 ; python_full_version < '3.11'
 attrs==26.1.0
 axe-selenium-python==2.1.6
 backports-asyncio-runner==1.2.0 ; python_full_version < '3.11'
-boto3==1.42.70
-botocore==1.42.70
+boto3==1.42.84
+botocore==1.42.84
 cachecontrol==0.14.4
 cachetools==7.0.5
 cattrs==26.1.0
@@ -36,8 +36,8 @@ fonttools==4.62.1
 frozenlist==1.8.0
 fsspec==2026.3.0
 gcsfs==2026.3.0
-google-api-core==2.30.2
-google-auth==2.49.1
+google-api-core==2.30.3
+google-auth==2.49.2
 google-auth-oauthlib==1.3.1
 google-cloud-core==2.5.1
 google-cloud-storage==3.10.1
@@ -45,7 +45,7 @@ google-cloud-storage-control==1.11.0
 google-crc32c==1.8.0
 google-resumable-media==2.8.2
 googleapis-common-protos==1.74.0
-greenlet==3.3.2
+greenlet==3.4.0
 grpc-google-iam-v1==0.14.4
 grpcio==1.80.0
 grpcio-status==1.80.0
@@ -65,8 +65,8 @@ jsonschema==4.26.0
 jsonschema-specifications==2025.9.1
 junit-xml==1.9
 kiwisolver==1.5.0
-librt==0.8.1 ; platform_python_implementation != 'PyPy'
-lxml==6.0.2
+librt==0.9.0 ; platform_python_implementation != 'PyPy'
+lxml==6.0.3
 markdown-it-py==3.0.0 ; python_full_version < '3.11'
 markdown-it-py==4.0.0 ; python_full_version >= '3.11'
 markupsafe==3.0.3
@@ -89,7 +89,7 @@ pathspec==1.0.4
 pfzy==0.3.4
 pillow==12.2.0
 pkce==1.0.3
-platformdirs==4.9.4
+platformdirs==4.9.6
 playwright==1.58.0
 pluggy==1.6.0
 port-for==1.0.0
@@ -108,7 +108,7 @@ pygments==2.20.0
 pyparsing==3.3.2
 pyshacl==0.31.0
 pysocks==1.7.1
-pytest==9.0.2
+pytest==9.0.3
 pytest-asyncio==1.3.0
 pytest-base-url==2.1.0
 pytest-cov==7.1.0
@@ -141,7 +141,7 @@ s3transfer==0.16.0
 schema-salad==8.9.20260327095315
 scipy==1.15.3 ; python_full_version < '3.11'
 scipy==1.17.1 ; python_full_version >= '3.11'
-selenium==4.41.0
+selenium==4.43.0
 seletools==1.5.0
 six==1.17.0
 sniffio==1.3.1
@@ -159,8 +159,8 @@ total-perspective-vortex==3.2.0
 trio==0.33.0
 trio-websocket==0.12.2
 tuspy==1.1.0
-types-cachetools==6.2.0.20260317
-types-requests==2.33.0.20260402
+types-cachetools==6.2.0.20260408
+types-requests==2.33.0.20260408
 typing-extensions==4.15.0
 typos==1.45.0
 tzdata==2026.1 ; sys_platform == 'win32'
diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
index 2ec79cb7773..a0b7244a362 100644
--- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
@@ -1,14 +1,14 @@
 # This file was autogenerated by uv via the following command:
 #    uv export --frozen --no-annotate --no-hashes --only-group=typecheck
 annotated-types==0.7.0
-boto3-stubs==1.42.83
+boto3-stubs==1.42.88
 botocore-stubs==1.42.41
 cffi==2.0.0 ; platform_python_implementation != 'PyPy'
 cryptography==46.0.7
-librt==0.8.1 ; platform_python_implementation != 'PyPy'
+librt==0.9.0 ; platform_python_implementation != 'PyPy'
 lxml-stubs==0.5.1
 mypy==1.20.0
-mypy-boto3-s3==1.42.80
+mypy-boto3-s3==1.42.85
 mypy-extensions==1.1.0
 pathspec==1.0.4
 pycparser==3.0 ; implementation_name != 'PyPy' and platform_python_implementation != 'PyPy'
@@ -16,22 +16,22 @@ pydantic==2.12.5
 pydantic-core==2.41.5
 tomli==2.4.1 ; python_full_version < '3.11'
 types-awscrt==0.31.3
-types-bleach==6.3.0.20260402
+types-bleach==6.3.0.20260408
 types-boto==2.49.18.20241019
 types-contextvars==2.4.7.3
 types-dataclasses==0.6.6
-types-docutils==0.22.3.20260322
-types-html5lib==1.1.11.20260402
-types-markdown==3.10.2.20260211
-types-paramiko==4.0.0.20260402
-types-python-dateutil==2.9.0.20260402
+types-docutils==0.22.3.20260408
+types-html5lib==1.1.11.20260408
+types-markdown==3.10.2.20260408
+types-paramiko==4.0.0.20260408
+types-python-dateutil==2.9.0.20260408
 types-python-slugify==8.0.2.20240310
-types-pyyaml==6.0.12.20250915
-types-requests==2.33.0.20260402
+types-pyyaml==6.0.12.20260408
+types-requests==2.33.0.20260408
 types-s3transfer==0.16.0
-types-setuptools==82.0.0.20260402
-types-six==1.17.0.20251009
-types-webencodings==0.5.0.20251108
+types-setuptools==82.0.0.20260408
+types-six==1.17.0.20260408
+types-webencodings==0.5.0.20260408
 typing-extensions==4.15.0
 typing-inspection==0.4.2
 urllib3==2.6.3