diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt
index 03721e47fc6..95f78eb5ac9 100644
--- a/lib/galaxy/dependencies/dev-requirements.txt
+++ b/lib/galaxy/dependencies/dev-requirements.txt
@@ -1,11 +1,11 @@
 # This file was autogenerated by uv via the following command:
 #    uv export --frozen --no-annotate --no-hashes --only-group=dev
-aiocop==1.1.4
+aiocop==1.1.5
 aiohappyeyeballs==2.7.1
-aiohttp==3.14.1
+aiohttp==3.14.3
 aiosignal==1.4.0
 alabaster==1.0.0
-annotated-types==0.7.0
+annotated-types==0.8.0
 ase==3.29.0
 ast-serialize==0.6.0
 async-timeout==5.0.1 ; python_full_version < '3.11'
@@ -20,16 +20,16 @@ boto3==1.43.46
 botocore==1.43.46
 build==1.5.0
 cachecontrol==0.14.4
-cachetools==7.1.4
+cachetools==7.1.6
 cattrs==26.1.0
-certifi==2026.6.17
+certifi==2026.7.22
 cffi==2.1.0 ; (implementation_name != 'pypy' and os_name == 'nt') or platform_python_implementation != 'PyPy'
 charset-normalizer==3.4.9
 click==8.4.2
 cloudbridge==4.3.0
 codespell==2.4.3
 colorama==0.4.6 ; os_name == 'nt' or sys_platform == 'win32'
-colorlog==6.11.0
+colorlog==6.12.0
 contourpy==1.3.2 ; python_full_version < '3.11'
 contourpy==1.3.3 ; python_full_version >= '3.11'
 coverage==7.15.2
@@ -45,15 +45,15 @@ docutils==0.22.4 ; python_full_version >= '3.11'
 dogpile-cache==1.5.0
 enum-tools==0.12.0
 exceptiongroup==1.3.1 ; python_full_version < '3.11'
-filelock==3.30.3
+filelock==3.32.0
 fluent-logger==0.11.1
 fonttools==4.63.0
 frozenlist==1.8.0
 fsspec==2026.6.0
 galaxy-release-util==0.3.3
 gcsfs==2026.7.0
-google-api-core==2.32.0
-google-auth==2.56.0
+google-api-core==2.33.0
+google-auth==2.56.2
 google-auth-oauthlib==1.4.0
 google-cloud-core==2.6.0
 google-cloud-storage==3.13.0
@@ -61,10 +61,10 @@ google-cloud-storage-control==1.12.0
 google-crc32c==1.8.0
 google-resumable-media==2.10.0
 googleapis-common-protos==1.75.0
-greenlet==3.5.3
+greenlet==3.5.4
 grpc-google-iam-v1==0.14.4
-grpcio==1.82.1
-grpcio-status==1.81.1
+grpcio==1.83.0
+grpcio-status==1.83.0
 h11==0.16.0
 html5rdf==1.2.1
 hvac==2.4.0
@@ -121,15 +121,15 @@ pathspec==1.1.1
 pfzy==0.3.4
 pillow==12.3.0
 pkce==1.0.3
-platformdirs==4.10.1
+platformdirs==4.11.0
 playwright==1.61.0
 pluggy==1.6.0
 port-for==1.0.0
 prettytable==3.18.0
 prompt-toolkit==3.0.52
 propcache==0.5.2
-proto-plus==1.28.1
-protobuf==6.33.6
+proto-plus==1.28.2
+protobuf==7.35.1
 psutil==7.2.2 ; sys_platform != 'cygwin'
 psycopg==3.3.4
 pyasn1==0.6.4
@@ -182,8 +182,8 @@ roman-numerals==4.1.0 ; python_full_version >= '3.11'
 rpds-py==0.30.0 ; python_full_version < '3.11'
 rpds-py==2026.6.3 ; python_full_version >= '3.11'
 ruamel-yaml==0.19.1
-rucio-clients==40.4.1
-s3transfer==0.19.1
+rucio-clients==41.0.0
+s3transfer==0.19.2
 schema-salad==8.9.20260417192335
 scipy==1.15.3 ; python_full_version < '3.11'
 scipy==1.17.1 ; python_full_version == '3.11.*'
@@ -234,5 +234,5 @@ wcwidth==0.8.2
 websocket-client==1.9.0
 werkzeug==3.1.8
 wsproto==1.3.2
-yarl==1.24.2
+yarl==1.24.5
 zipp==4.1.0 ; python_full_version < '3.12'
diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt
index cc063beb0db..882129ca099 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==0.15.22
+ruff==0.16.0
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index 1ca9800b136..bee74d005c7 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -7,14 +7,14 @@ aiofile==3.9.0 ; python_full_version < '3.11'
 aiofile==3.11.1 ; python_full_version >= '3.11'
 aiofiles==25.1.0
 aiohappyeyeballs==2.7.1
-aiohttp==3.14.1
+aiohttp==3.14.3
 aioitertools==0.13.0
 aiosignal==1.4.0
 alembic==1.18.5
 amqp==5.3.1
 annotated-doc==0.0.4
-annotated-types==0.7.0
-anthropic==0.117.0
+annotated-types==0.8.0
+anthropic==0.120.0
 anyio==4.14.2
 apispec==6.10.0
 appdirs==1.4.4
@@ -40,10 +40,10 @@ boto==2.49.0
 botocore==1.43.46
 bx-python==0.14.0
 cachecontrol==0.14.4
-cachetools==7.1.4
+cachetools==7.1.6
 caio==0.9.25
 celery==5.6.3
-certifi==2026.6.17
+certifi==2026.7.22
 cffi==2.1.0 ; implementation_name == 'pypy' or platform_python_implementation != 'PyPy'
 charset-normalizer==3.4.9
 circus==0.19.0
@@ -59,8 +59,8 @@ cryptography==49.0.0
 ct3==3.4.0.post5
 cwl-upgrader==1.2.15
 cwl-utils==0.42
-cwltool==3.2.20260413085819
-cyclopts==4.21.1
+cwltool==3.2.20260720092025
+cyclopts==4.22.2
 defusedxml==0.7.1
 deprecated==1.3.1
 dictobj==0.4
@@ -76,36 +76,36 @@ email-validator==2.3.0
 et-xmlfile==2.0.0
 exceptiongroup==1.3.1
 executing==2.2.1
-fastapi==0.139.2
+fastapi==0.140.0
 fastmcp==3.4.4
 fastmcp-slim==3.4.4
-filelock==3.30.3
+filelock==3.32.0
 fissix==24.4.24
 frozenlist==1.8.0
 fs==2.4.16
 fsspec==2026.6.0
 future==1.0.0
-genai-prices==0.0.71
-google-api-core==2.32.0
-google-auth==2.56.0
+genai-prices==0.0.72
+google-api-core==2.33.0
+google-auth==2.56.2
 google-cloud-batch==0.22.1
-google-genai==2.11.0
+google-genai==2.14.0
 googleapis-common-protos==1.75.0
 gravity==1.2.3
-greenlet==3.5.3 ; 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==3.5.4 ; 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==2.1.0
-grpcio==1.82.1
-grpcio-status==1.81.1
+grpcio==1.83.0
+grpcio-status==1.83.0
 gunicorn==26.0.0
 gxformat2==0.27.0
 h11==0.16.0
 h5grove==4.0.0
 h5py==3.16.0
 httpcore==1.0.9
-httpcore2==2.7.0
+httpcore2==2.9.1
 httpx==0.28.1
 httpx-sse==0.4.3
-httpx2==2.7.0
+httpx2==2.9.1
 humanfriendly==10.0
 idna==3.18
 ijson==3.5.1
@@ -122,7 +122,7 @@ jeepney==0.9.0 ; sys_platform == 'linux'
 jinja2==3.1.6
 jiter==0.16.0
 jmespath==1.1.0
-joserfc==1.7.3
+joserfc==1.7.4
 jsonref==1.1.0
 jsonschema==4.26.0
 jsonschema-path==0.5.0
@@ -132,8 +132,8 @@ kombu==5.6.2
 lagom==2.7.7
 legacy-cgi==2.6.4 ; python_full_version >= '3.13'
 limits==5.8.0
-logfire==4.37.0
-logfire-api==4.37.0
+logfire==4.39.0
+logfire-api==4.39.0
 lxml==6.1.1
 mako==1.3.12
 markdown==3.10.2
@@ -158,31 +158,31 @@ numpy==2.2.6 ; python_full_version < '3.11'
 numpy==2.4.6 ; python_full_version == '3.11.*'
 numpy==2.5.1 ; python_full_version >= '3.12'
 oauthlib==3.3.1
-openai==2.46.0
+openai==2.48.0
 openapi-pydantic==0.5.1
 openpyxl==3.1.5
-opentelemetry-api==1.42.1
-opentelemetry-exporter-otlp-proto-common==1.42.1
-opentelemetry-exporter-otlp-proto-http==1.42.1
-opentelemetry-instrumentation==0.63b1
-opentelemetry-instrumentation-httpx==0.63b1
-opentelemetry-proto==1.42.1
-opentelemetry-sdk==1.42.1
-opentelemetry-semantic-conventions==0.63b1
-opentelemetry-util-http==0.63b1
+opentelemetry-api==1.44.0
+opentelemetry-exporter-otlp-proto-common==1.44.0
+opentelemetry-exporter-otlp-proto-http==1.44.0
+opentelemetry-instrumentation==0.65b0
+opentelemetry-instrumentation-httpx==0.65b0
+opentelemetry-proto==1.44.0
+opentelemetry-sdk==1.44.0
+opentelemetry-semantic-conventions==0.65b0
+opentelemetry-util-http==0.65b0
 orjson==3.11.9
 packaging==26.2
 paramiko==5.0.0
 parsley==1.3
 paste==3.10.1
 pathable==0.6.0
-pebble==5.2.0
+pebble==5.2.1
 pillow==12.3.0
-platformdirs==4.10.1
+platformdirs==4.11.0
 prompt-toolkit==3.0.52
 propcache==0.5.2
-proto-plus==1.28.1
-protobuf==6.33.6
+proto-plus==1.28.2
+protobuf==7.35.1
 prov==1.5.1
 psutil==7.2.2
 pulsar-galaxy-lib==0.15.15
@@ -193,12 +193,12 @@ 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==2.13.4
-pydantic-ai==2.13.0
-pydantic-ai-slim==2.13.0
+pydantic-ai==2.18.0
+pydantic-ai-slim==2.18.0
 pydantic-core==2.46.4
-pydantic-evals==2.13.0
+pydantic-evals==2.18.0
 pydantic-extra-types==2.11.1
-pydantic-graph==2.13.0
+pydantic-graph==2.18.0
 pydantic-settings==2.14.2
 pydantic-tes==0.4.0
 pydicom==3.0.2
@@ -228,7 +228,7 @@ pyzmq==27.1.0
 rdflib==7.6.0
 referencing==0.37.0
 refgenconf==0.13.1
-regex==2026.7.10
+regex==2026.7.19
 repoze-lru==0.8
 requests==2.34.2
 requests-oauthlib==2.0.0
@@ -254,7 +254,7 @@ sortedcontainers==2.4.0
 spython==0.3.14
 sqlalchemy==2.0.51
 sqlparse==0.5.5
-sse-starlette==3.4.5
+sse-starlette==3.4.6
 starlette==1.3.1
 starlette-context==0.5.1
 supervisor==4.3.0
@@ -268,7 +268,7 @@ tiktoken==0.13.0
 tinydb==4.8.2
 tomli==2.4.1 ; python_full_version < '3.11'
 tornado==6.5.7
-tqdm==4.69.0
+tqdm==4.69.1
 truststore==0.10.4
 tuspy==1.1.0
 tuspyserver==4.2.12
@@ -290,6 +290,6 @@ websockets==16.1.1
 whoosh==2.7.4
 wrapt==2.2.2
 yacman==1.0.0
-yarl==1.24.2
+yarl==1.24.5
 zipp==4.1.0 ; python_full_version < '3.12'
 zipstream-new==1.1.8
diff --git a/lib/galaxy/dependencies/pinned-test-requirements.txt b/lib/galaxy/dependencies/pinned-test-requirements.txt
index 61d66eb08ec..892963bd00f 100644
--- a/lib/galaxy/dependencies/pinned-test-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-test-requirements.txt
@@ -1,10 +1,10 @@
 # This file was autogenerated by uv via the following command:
 #    uv export --frozen --no-annotate --no-hashes --only-group=test
-aiocop==1.1.4
+aiocop==1.1.5
 aiohappyeyeballs==2.7.1
-aiohttp==3.14.1
+aiohttp==3.14.3
 aiosignal==1.4.0
-annotated-types==0.7.0
+annotated-types==0.8.0
 ase==3.29.0
 ast-serialize==0.6.0
 async-timeout==5.0.1 ; python_full_version < '3.11'
@@ -15,15 +15,15 @@ backports-asyncio-runner==1.2.0 ; python_full_version < '3.11'
 boto3==1.43.46
 botocore==1.43.46
 cachecontrol==0.14.4
-cachetools==7.1.4
+cachetools==7.1.6
 cattrs==26.1.0
-certifi==2026.6.17
+certifi==2026.7.22
 cffi==2.1.0 ; (implementation_name != 'pypy' and os_name == 'nt') or platform_python_implementation != 'PyPy'
 charset-normalizer==3.4.9
 click==8.4.2
 cloudbridge==4.3.0
 colorama==0.4.6 ; sys_platform == 'win32'
-colorlog==6.11.0
+colorlog==6.12.0
 contourpy==1.3.2 ; python_full_version < '3.11'
 contourpy==1.3.3 ; python_full_version >= '3.11'
 coverage==7.15.2
@@ -35,14 +35,14 @@ defusedxml==0.7.1
 dogpile-cache==1.5.0
 enum-tools==0.12.0
 exceptiongroup==1.3.1 ; python_full_version < '3.11'
-filelock==3.30.3
+filelock==3.32.0
 fluent-logger==0.11.1
 fonttools==4.63.0
 frozenlist==1.8.0
 fsspec==2026.6.0
 gcsfs==2026.7.0
-google-api-core==2.32.0
-google-auth==2.56.0
+google-api-core==2.33.0
+google-auth==2.56.2
 google-auth-oauthlib==1.4.0
 google-cloud-core==2.6.0
 google-cloud-storage==3.13.0
@@ -50,10 +50,10 @@ google-cloud-storage-control==1.12.0
 google-crc32c==1.8.0
 google-resumable-media==2.10.0
 googleapis-common-protos==1.75.0
-greenlet==3.5.3
+greenlet==3.5.4
 grpc-google-iam-v1==0.14.4
-grpcio==1.82.1
-grpcio-status==1.81.1
+grpcio==1.83.0
+grpcio-status==1.83.0
 h11==0.16.0
 html5rdf==1.2.1
 hvac==2.4.0
@@ -96,15 +96,15 @@ pathspec==1.1.1
 pfzy==0.3.4
 pillow==12.3.0
 pkce==1.0.3
-platformdirs==4.10.1
+platformdirs==4.11.0
 playwright==1.61.0
 pluggy==1.6.0
 port-for==1.0.0
 prettytable==3.18.0
 prompt-toolkit==3.0.52
 propcache==0.5.2
-proto-plus==1.28.1
-protobuf==6.33.6
+proto-plus==1.28.2
+protobuf==7.35.1
 psutil==7.2.2 ; sys_platform != 'cygwin'
 psycopg==3.3.4
 pyasn1==0.6.4
@@ -147,8 +147,8 @@ roc-validator==0.11.2
 rpds-py==0.30.0 ; python_full_version < '3.11'
 rpds-py==2026.6.3 ; python_full_version >= '3.11'
 ruamel-yaml==0.19.1
-rucio-clients==40.4.1
-s3transfer==0.19.1
+rucio-clients==41.0.0
+s3transfer==0.19.2
 schema-salad==8.9.20260417192335
 scipy==1.15.3 ; python_full_version < '3.11'
 scipy==1.17.1 ; python_full_version == '3.11.*'
@@ -185,5 +185,5 @@ wcwidth==0.8.2
 websocket-client==1.9.0
 werkzeug==3.1.8
 wsproto==1.3.2
-yarl==1.24.2
+yarl==1.24.5
 zipp==4.1.0 ; python_full_version < '3.12'
diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
index 67342497161..267260e10e3 100644
--- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
@@ -1,8 +1,8 @@
 # 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
+annotated-types==0.8.0
 ast-serialize==0.6.0
-boto3-stubs==1.43.51
+boto3-stubs==1.43.56
 botocore-stubs==1.43.14
 cffi==2.1.0 ; platform_python_implementation != 'PyPy'
 cryptography==49.0.0
@@ -22,17 +22,17 @@ types-boto==2.49.18.20241019
 types-cachetools==7.0.0.20260713
 types-contextvars==2.4.7.3
 types-dataclasses==0.6.6
-types-docutils==0.22.3.20260712
+types-docutils==0.22.3.20260724
 types-html5lib==1.1.11.20260518
 types-markdown==3.10.2.20260712
-types-paramiko==5.0.0.20260617
+types-paramiko==5.0.0.20260724
 types-python-dateutil==2.9.0.20260716
 types-python-slugify==8.0.2.20240310
-types-pyyaml==6.0.12.20260518
+types-pyyaml==6.0.12.20260724
 types-requests==2.33.0.20260712
 types-s3transfer==0.16.0
-types-setuptools==83.0.0.20260716
-types-six==1.17.0.20260518
+types-setuptools==83.0.0.20260724
+types-six==1.17.0.20260724
 types-webencodings==0.5.0.20260408
 typing-extensions==4.16.0
 typing-inspection==0.4.2