From 19bdb951f236415968f5d0d0599cb657b56bc460 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 1 May 2026 18:18:01 +0000
Subject: [PATCH 1/3] Initial plan


From 4f01d899f5485c64e9ea24fe811cb6235284d27d Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 1 May 2026 18:18:47 +0000
Subject: [PATCH 2/3] Fix Apptainer install: drop PPA, simplify cache, update
 actions/cache to v4

Agent-Logs-Url: https://github.com/sequana/fastqc/sessions/38342296-c34c-41d3-a540-a778e799f58f

Co-authored-by: cokelaer <778821+cokelaer@users.noreply.github.com>
---
 .github/workflows/apptainer.yml | 35 +++++++--------------------------
 1 file changed, 7 insertions(+), 28 deletions(-)

diff --git a/.github/workflows/apptainer.yml b/.github/workflows/apptainer.yml
index c5e9a65..593f4a7 100644
--- a/.github/workflows/apptainer.yml
+++ b/.github/workflows/apptainer.yml
@@ -28,40 +28,19 @@ jobs:
         sudo rm -rf /usr/share/dotnet
         sudo rm -rf "$AGENT_TOOLSDIRECTORY"
 
-    # Cache APT .deb packages
-    - name: Cache APT archives
-      uses: actions/cache@v3
-      with:
-        path: /var/cache/apt/archives
-        key: ${{ runner.os }}-apt-cache-v1
-
-    # Cache Apptainer installation
-    - name: Cache Apptainer install
-      id: cache-apptainer
-      uses: actions/cache@v3
+    # Cache Apptainer image cache (~/.apptainer/cache)
+    - name: Cache Apptainer images
+      uses: actions/cache@v4
       with:
-        path: |
-          /usr/bin/apptainer
-          /usr/lib/apptainer
-          /etc/apptainer
-        key: ${{ runner.os }}-apptainer-v1
+        path: ~/.apptainer/cache
+        key: ${{ runner.os }}-apptainer-images-v1
 
-    # Install Apptainer only if not cached
+    # Install Apptainer from the default Ubuntu apt repositories
     - name: Install Apptainer
-      if: steps.cache-apptainer.outputs.cache-hit != 'true'
       run: |
-        sudo apt-get update
-        sudo apt-get install -y software-properties-common
-        sudo add-apt-repository -y ppa:apptainer/ppa
         sudo apt-get update
         sudo apt-get install -y apptainer
-
-    # Cache Apptainer image cache (~/.apptainer/cache)
-    - name: Cache Apptainer images
-      uses: actions/cache@v3
-      with:
-        path: ~/.apptainer/cache
-        key: ${{ runner.os }}-apptainer-images-v1
+        apptainer --version
 
     # Checkout repository
     - name: Checkout repo

From 90a6d4f2e1f90ee26b8dd3177c9886776e3ffd07 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 1 May 2026 18:22:58 +0000
Subject: [PATCH 3/3] Fix Apptainer install: download .deb from GitHub releases
 instead of apt

Agent-Logs-Url: https://github.com/sequana/fastqc/sessions/b2f06054-8950-48ef-b7e1-9d770e590ca1

Co-authored-by: cokelaer <778821+cokelaer@users.noreply.github.com>
---
 .github/workflows/apptainer.yml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/apptainer.yml b/.github/workflows/apptainer.yml
index 593f4a7..3180cba 100644
--- a/.github/workflows/apptainer.yml
+++ b/.github/workflows/apptainer.yml
@@ -35,11 +35,13 @@ jobs:
         path: ~/.apptainer/cache
         key: ${{ runner.os }}-apptainer-images-v1
 
-    # Install Apptainer from the default Ubuntu apt repositories
+    # Install Apptainer from GitHub releases (avoids flaky Launchpad PPA)
     - name: Install Apptainer
       run: |
-        sudo apt-get update
-        sudo apt-get install -y apptainer
+        APPTAINER_VERSION=$(curl -s https://api.github.com/repos/apptainer/apptainer/releases/latest \
+          | grep '"tag_name"' | cut -d'"' -f4 | sed 's/v//')
+        wget -q "https://github.com/apptainer/apptainer/releases/download/v${APPTAINER_VERSION}/apptainer_${APPTAINER_VERSION}_amd64.deb"
+        sudo apt-get install -y "./apptainer_${APPTAINER_VERSION}_amd64.deb"
         apptainer --version
 
     # Checkout repository