diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index 777d5d6..90eb755 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -54,7 +54,7 @@ jobs:
 
       - name: Install libcurl-dev for pycurl (needed by arvados)
         if: ${{ matrix.step == 'mypy' }}
-        run: sudo apt-get install -y --no-install-recommends libcurl4-gnutls-dev gnutls-dev
+        run: sudo apt-get update && sudo apt-get install -y --no-install-recommends libcurl4-gnutls-dev gnutls-dev
 
       - name: Upgrade setuptools and install tox
         run: |
diff --git a/lint-requirements.txt b/lint-requirements.txt
index f4a2d26..9f1cc7e 100644
--- a/lint-requirements.txt
+++ b/lint-requirements.txt
@@ -1,4 +1,4 @@
 flake8-bugbear < 24.13
-black ~= 25.1
+black ~= 25.9
 codespell
 isort >= 5
diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index 9fbd8f6..6dac953 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.15
+mypy==1.18.2
 types-PyYAML
 types-requests
 types-setuptools
diff --git a/pyproject.toml b/pyproject.toml
index 96b4578..c018d3b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -40,7 +40,7 @@ Download = "https://github.com/common-workflow-language/cwltool-service/releases%20[project.optional-dependencies]%20cwltool%20=%20["cwlref-runner"]
 arvados = ["arvados-cwl-runner"]
-toil = ["toil[cwl]==8.2.0"]
+toil = ["toil[cwl]==9.1.2"]
 
 [project.scripts]
 wes-server = "wes_service.wes_service_main:main"