From 5bcec2f37ef68d3d3a5a518c568a217a925c049f Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Tue, 25 Aug 2026 19:33:37 +0200
Subject: [PATCH 1/2] update to 26.08

---
 Dockerfile       | 8 ++++----
 requirements.txt | 1 -
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 6eb4dbb..ed626e3 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,11 +1,11 @@
 # RStudio container used for Galaxy RStudio Integration
 
-FROM rocker/rstudio:4.4
+FROM rocker/rstudio:4.5
 
-ARG CONDA_VERSION=24.11.2
-ARG SUFFIX=1
+ARG CONDA_VERSION=26.5.3
+ARG SUFFIX=0
 ARG MINIFORGE_VERSION=${CONDA_VERSION}-${SUFFIX}
-ARG R_VERSION=4.4
+ARG R_VERSION=4.5
 
 ENV CONDA_PATH=/opt/miniconda \
     MINICONDA_BIN_DIR="/opt/miniconda/bin" \
diff --git a/requirements.txt b/requirements.txt
index 057c04e..9bd0f44 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -36,7 +36,6 @@ bioconductor-gviz
 bioconductor-rgraphviz
 bioconductor-limma
 bioconductor-deseq2
-bioconductor-cummerbund
 bioconductor-affy
 bioconductor-rsamtools
 

From 435e61cfd3812391e17b3b471a64900555d49a1e Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Tue, 25 Aug 2026 19:51:47 +0200
Subject: [PATCH 2/2] add CI

---
 .github/workflows/pr.yml      | 32 ++++++++++++++++++++++++++++++++
 .github/workflows/release.yml | 34 ++++++++++++++++++++++++++++++++++
 2 files changed, 66 insertions(+)
 create mode 100644 .github/workflows/pr.yml
 create mode 100644 .github/workflows/release.yml

diff --git a/.github/workflows/pr.yml b/.github/workflows/pr.yml
new file mode 100644
index 0000000..ba476ec
--- /dev/null
+++ b/.github/workflows/pr.yml
@@ -0,0 +1,32 @@
+name: PR
+
+on:
+  pull_request:
+    branches: [ "main", "master" ]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  initialise:
+    runs-on: ubuntu-latest
+
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v3
+        with:
+          submodules: recursive
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+  build_only:
+    needs: initialise
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Build docker image
+        uses: docker/build-push-action@v4
+        with:
+          push: false
+          tags: user/app:latest
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
new file mode 100644
index 0000000..cee04d6
--- /dev/null
+++ b/.github/workflows/release.yml
@@ -0,0 +1,34 @@
+name: release-CI
+
+on:
+  release:
+    types: [published]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  build_and_publish:
+    runs-on: ubuntu-latest
+
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v3
+        with:
+          submodules: recursive
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Login to Quay IO
+        uses: docker/login-action@v2
+        with:
+          registry: quay.io
+          username: '$oauthtoken'
+          password: ${{ secrets.QUAY_OAUTH_TOKEN }}
+
+      - name: Build docker image and push to quay.io
+        uses: docker/build-push-action@v4
+        with:
+          push: true
+          tags: quay.io/galaxy/rstudio-notebook:${{ github.event.release.tag_name }}