From 7df0a7e004959726f605a59eb51f02ba6c94a463 Mon Sep 17 00:00:00 2001
From: Oliver Pain <43761992+opain@users.noreply.github.com>
Date: Thu, 17 Jul 2025 08:32:43 +0100
Subject: [PATCH 1/7] Update build_deploy_container.yaml

---
 .github/workflows/build_deploy_container.yaml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/.github/workflows/build_deploy_container.yaml b/.github/workflows/build_deploy_container.yaml
index 48290ea..8cfa49a 100644
--- a/.github/workflows/build_deploy_container.yaml
+++ b/.github/workflows/build_deploy_container.yaml
@@ -30,6 +30,13 @@ jobs:
     - name: Checkout code
       uses: actions/checkout@v2
 
+    - name: Maximize build disk space
+      uses: easimon/maximize-build-space@v10
+      with:
+        root-reserve-mb: 512
+        swap-size-mb: 1024
+        remove-dotnet: 'true'
+        
     - name: Export Secrets to Environment
       run: |
         echo "SINGULARITY_LIBRARY_TOKEN=${{ secrets.SINGULARITY_LIBRARY_TOKEN }}" >> $GITHUB_ENV

From 20c03a5becde068422559144bf9b19f849620e41 Mon Sep 17 00:00:00 2001
From: Oliver Pain <43761992+opain@users.noreply.github.com>
Date: Thu, 17 Jul 2025 08:43:38 +0100
Subject: [PATCH 2/7] Update build_deploy_container.yaml

---
 .github/workflows/build_deploy_container.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/build_deploy_container.yaml b/.github/workflows/build_deploy_container.yaml
index 8cfa49a..39db604 100644
--- a/.github/workflows/build_deploy_container.yaml
+++ b/.github/workflows/build_deploy_container.yaml
@@ -27,16 +27,16 @@ jobs:
       DOCKERFILE_PATH: pipeline/misc/docker/Dockerfile
 
     steps:
-    - name: Checkout code
-      uses: actions/checkout@v2
-
     - name: Maximize build disk space
       uses: easimon/maximize-build-space@v10
       with:
         root-reserve-mb: 512
         swap-size-mb: 1024
         remove-dotnet: 'true'
-        
+
+    - name: Checkout code
+      uses: actions/checkout@v2
+      
     - name: Export Secrets to Environment
       run: |
         echo "SINGULARITY_LIBRARY_TOKEN=${{ secrets.SINGULARITY_LIBRARY_TOKEN }}" >> $GITHUB_ENV

From d5f12a6e570d412da1d680d64467495c2b15b9ef Mon Sep 17 00:00:00 2001
From: Oliver Pain <43761992+opain@users.noreply.github.com>
Date: Thu, 17 Jul 2025 08:52:32 +0100
Subject: [PATCH 3/7] Update Dockerfile

---
 pipeline/misc/docker/Dockerfile | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/pipeline/misc/docker/Dockerfile b/pipeline/misc/docker/Dockerfile
index 58fe319..5273464 100644
--- a/pipeline/misc/docker/Dockerfile
+++ b/pipeline/misc/docker/Dockerfile
@@ -10,10 +10,10 @@ RUN apt-get update && \
     echo 'exec /bin/tar --no-same-owner "$@"' >> /usr/local/bin/tar && \
     chmod +x /usr/local/bin/tar
 
-# Install Mambaforge
-RUN wget https://github.com/conda-forge/miniforge/releases/download/4.10.3-10/Mambaforge-4.10.3-10-Linux-x86_64.sh && \
-    bash Mambaforge-4.10.3-10-Linux-x86_64.sh -b -p /opt/mambaforge && \
-    rm Mambaforge-4.10.3-10-Linux-x86_64.sh
+# Install Miniforge
+RUN wget https://github.com/conda-forge/miniforge/releases/download/24.11.3-0/Miniforge3-24.11.3-0-Linux-x86_64.sh && \
+    bash Miniforge3-24.11.3-0-Linux-x86_64.sh -b -p /opt/miniforge && \
+    rm Miniforge3-24.11.3-0-Linux-x86_64.sh
 
 # Download GenoPred
 RUN mkdir -p /tools/GenoPred && \
@@ -22,20 +22,20 @@ RUN mkdir -p /tools/GenoPred && \
     git fetch --tags
 
 # Create genopred env
-RUN /opt/mambaforge/bin/conda init bash && \
-    echo "source /opt/mambaforge/etc/profile.d/conda.sh" >> /etc/bash.bashrc && \
-    . /opt/mambaforge/etc/profile.d/conda.sh && \
+RUN /opt/miniforge/bin/conda init bash && \
+    echo "source /opt/miniforge/etc/profile.d/conda.sh" >> /etc/bash.bashrc && \
+    . /opt/miniforge/etc/profile.d/conda.sh && \
     mamba env update -n genopred -f /tools/GenoPred/pipeline/envs/pipeline.yaml && \
     mamba clean -a -y
 
 # Run initial snakemake command to setup dependencies
-RUN /opt/mambaforge/bin/conda init bash && \
-    echo "source /opt/mambaforge/etc/profile.d/conda.sh" >> /etc/bash.bashrc && \
-    . /opt/mambaforge/etc/profile.d/conda.sh && \
+RUN /opt/miniforge/bin/conda init bash && \
+    echo "source /opt/miniforge/etc/profile.d/conda.sh" >> /etc/bash.bashrc && \
+    . /opt/miniforge/etc/profile.d/conda.sh && \
     conda activate genopred && \
     cd /tools/GenoPred/pipeline && \
     snakemake --restart-times 3 -j1 --use-conda --conda-frontend mamba install_r_packages resources/software/pgscatalog_utils/download_pgscatalog_utils.done && \
     mamba clean -a -y
 
 ENTRYPOINT ["/bin/bash"]
-CMD ["-c", "source /opt/mambaforge/etc/profile.d/conda.sh && conda init && source ~/.bashrc && conda activate genopred && cd /tools/GenoPred/pipeline && exec /bin/bash"]
+CMD ["-c", "source /opt/miniforge/etc/profile.d/conda.sh && conda init && source ~/.bashrc && conda activate genopred && cd /tools/GenoPred/pipeline && exec /bin/bash"]

From fb01408bdd21560dbb8755183aab8954547b1608 Mon Sep 17 00:00:00 2001
From: Oliver Pain <43761992+opain@users.noreply.github.com>
Date: Thu, 17 Jul 2025 09:01:52 +0100
Subject: [PATCH 4/7] Update build_deploy_container.yaml

---
 .github/workflows/build_deploy_container.yaml | 54 +++++++++----------
 1 file changed, 24 insertions(+), 30 deletions(-)

diff --git a/.github/workflows/build_deploy_container.yaml b/.github/workflows/build_deploy_container.yaml
index 39db604..668f930 100644
--- a/.github/workflows/build_deploy_container.yaml
+++ b/.github/workflows/build_deploy_container.yaml
@@ -27,13 +27,6 @@ jobs:
       DOCKERFILE_PATH: pipeline/misc/docker/Dockerfile
 
     steps:
-    - name: Maximize build disk space
-      uses: easimon/maximize-build-space@v10
-      with:
-        root-reserve-mb: 512
-        swap-size-mb: 1024
-        remove-dotnet: 'true'
-
     - name: Checkout code
       uses: actions/checkout@v2
       
@@ -56,34 +49,33 @@ jobs:
           echo "::set-output name=tag::${{ github.event.inputs.tag || github.sha }}"
         fi
 
-    - name: Build docker container
-      run: |
-        docker buildx build --platform linux/amd64 -f $DOCKERFILE_PATH -t $DOCKER_IMAGE_NAME:latest -t $DOCKER_IMAGE_NAME:${{ steps.set_tag.outputs.tag }} --push .
+#    - name: Build docker container
+#      run: |
+#        docker buildx build --platform linux/amd64 -f $DOCKERFILE_PATH -t $DOCKER_IMAGE_NAME:latest -t $DOCKER_IMAGE_NAME:${{ steps.set_tag.outputs.tag }} --push .
 
-    - name: Clean up Docker build artifacts
-      run: |
-        docker system prune -af
-  
+    - name: Maximize build disk space
+      uses: easimon/maximize-build-space@v10
+      with:
+        root-reserve-mb: 512
+        swap-size-mb: 1024
+        remove-dotnet: 'true'
+          
     - name: Setup Apptainer
       uses: eWaterCycle/setup-apptainer@v2.0.0
 
     - name: Configure Singularity temp directories
       run: |
-        # create a temp area inside the GitHub runner's large temp folder
-        mkdir -p $RUNNER_TEMP/singularity
+        mkdir -p "$RUNNER_TEMP/singularity/cache"
         echo "APPTAINER_TMPDIR=$RUNNER_TEMP/singularity" >> $GITHUB_ENV
-        # optional: keep a separate cache dir
-        mkdir -p $RUNNER_TEMP/singularity/cache
         echo "APPTAINER_CACHEDIR=$RUNNER_TEMP/singularity/cache" >> $GITHUB_ENV
-        
-    - name: Check free space
-      run: |
-        df -h
-  
+    
     - name: Convert Docker Image to Singularity SIF
       run: |
-        apptainer pull --disable-cache --tmpdir $RUNNER_TEMP/singularity /mnt/genopred_image.sif docker://${DOCKER_IMAGE_NAME}:latest
-
+        apptainer pull --disable-cache \
+          --tmpdir "$RUNNER_TEMP/singularity" \
+          "$GITHUB_WORKSPACE/genopred_image.sif" \
+          docker://${DOCKER_IMAGE_NAME}:latest
+      
     - name: Install expect
       run: |
         sudo apt-get update
@@ -105,14 +97,16 @@ jobs:
         send -- "${{ secrets.SIGNING_KEY_PASSWORD }}\r"
         expect eof
         '
+        
     - name: Sign the Singularity Image
       run: |
         expect -c '
-        spawn apptainer sign /mnt/genopred_image.sif
-        expect "Enter your key passphrase : "
-        send -- "${{ secrets.SIGNING_KEY_PASSWORD }}\r"
-        expect eof
+          spawn apptainer sign "$GITHUB_WORKSPACE/genopred_image.sif"
+          expect "Enter your key passphrase : "
+          send -- "${{ secrets.SIGNING_KEY_PASSWORD }}\r"
+          expect eof
         '
+        
     - name: Create Token File
       run: echo "${{ secrets.SINGULARITY_LIBRARY_TOKEN }}" > tokenfile
 
@@ -124,7 +118,7 @@ jobs:
 
     - name: Push Singularity Image to Singularity Library
       run: |
-        apptainer push /mnt/genopred_image.sif $SINGULARITY_IMAGE_NAME:latest
+        apptainer push "$GITHUB_WORKSPACE/genopred_image.sif" "$SINGULARITY_IMAGE_NAME:latest"
 
     - name: Setup tmate session
       if: ${{ failure() }}

From 31d4ec5ae68c28b9d27da366e8b72c238e0df64f Mon Sep 17 00:00:00 2001
From: Oliver Pain <43761992+opain@users.noreply.github.com>
Date: Thu, 17 Jul 2025 09:06:48 +0100
Subject: [PATCH 5/7] Update build_deploy_container.yaml

---
 .github/workflows/build_deploy_container.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/build_deploy_container.yaml b/.github/workflows/build_deploy_container.yaml
index 668f930..246dc65 100644
--- a/.github/workflows/build_deploy_container.yaml
+++ b/.github/workflows/build_deploy_container.yaml
@@ -65,14 +65,14 @@ jobs:
 
     - name: Configure Singularity temp directories
       run: |
-        mkdir -p "$RUNNER_TEMP/singularity/cache"
-        echo "APPTAINER_TMPDIR=$RUNNER_TEMP/singularity" >> $GITHUB_ENV
-        echo "APPTAINER_CACHEDIR=$RUNNER_TEMP/singularity/cache" >> $GITHUB_ENV
+        mkdir -p "$GITHUB_WORKSPACE/.singularity/cache"
+        echo "APPTAINER_TMPDIR=$GITHUB_WORKSPACE/.singularity" >> $GITHUB_ENV
+        echo "APPTAINER_CACHEDIR=$GITHUB_WORKSPACE/.singularity/cache" >> $GITHUB_ENV
     
     - name: Convert Docker Image to Singularity SIF
       run: |
         apptainer pull --disable-cache \
-          --tmpdir "$RUNNER_TEMP/singularity" \
+          --tmpdir "$GITHUB_WORKSPACE/.singularity" \
           "$GITHUB_WORKSPACE/genopred_image.sif" \
           docker://${DOCKER_IMAGE_NAME}:latest
       

From b8393a0c4f680b28cbad07a190947002c4ad5a9d Mon Sep 17 00:00:00 2001
From: Oliver Pain <43761992+opain@users.noreply.github.com>
Date: Thu, 17 Jul 2025 09:23:19 +0100
Subject: [PATCH 6/7] Update build_deploy_container.yaml

---
 .github/workflows/build_deploy_container.yaml | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/build_deploy_container.yaml b/.github/workflows/build_deploy_container.yaml
index 246dc65..8138121 100644
--- a/.github/workflows/build_deploy_container.yaml
+++ b/.github/workflows/build_deploy_container.yaml
@@ -100,12 +100,13 @@ jobs:
         
     - name: Sign the Singularity Image
       run: |
-        expect -c '
-          spawn apptainer sign "$GITHUB_WORKSPACE/genopred_image.sif"
-          expect "Enter your key passphrase : "
-          send -- "${{ secrets.SIGNING_KEY_PASSWORD }}\r"
+        SIF_PATH="$GITHUB_WORKSPACE/genopred_image.sif"
+        expect -c "
+          spawn apptainer sign \"$SIF_PATH\"
+          expect \"Enter your key passphrase : \"
+          send -- \"${{ secrets.SIGNING_KEY_PASSWORD }}\r\"
           expect eof
-        '
+        "
         
     - name: Create Token File
       run: echo "${{ secrets.SINGULARITY_LIBRARY_TOKEN }}" > tokenfile

From 35cf09cbf413f90f0aa987d7171e00bfe5e45c67 Mon Sep 17 00:00:00 2001
From: Oliver Pain <43761992+opain@users.noreply.github.com>
Date: Thu, 17 Jul 2025 09:47:50 +0100
Subject: [PATCH 7/7] Update build_deploy_container.yaml

---
 .github/workflows/build_deploy_container.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build_deploy_container.yaml b/.github/workflows/build_deploy_container.yaml
index 8138121..2d3eb93 100644
--- a/.github/workflows/build_deploy_container.yaml
+++ b/.github/workflows/build_deploy_container.yaml
@@ -49,9 +49,9 @@ jobs:
           echo "::set-output name=tag::${{ github.event.inputs.tag || github.sha }}"
         fi
 
-#    - name: Build docker container
-#      run: |
-#        docker buildx build --platform linux/amd64 -f $DOCKERFILE_PATH -t $DOCKER_IMAGE_NAME:latest -t $DOCKER_IMAGE_NAME:${{ steps.set_tag.outputs.tag }} --push .
+    - name: Build docker container
+      run: |
+        docker buildx build --platform linux/amd64 -f $DOCKERFILE_PATH -t $DOCKER_IMAGE_NAME:latest -t $DOCKER_IMAGE_NAME:${{ steps.set_tag.outputs.tag }} --push .
 
     - name: Maximize build disk space
       uses: easimon/maximize-build-space@v10