From 8b6743a3c538a2296640a1cb2422e420f4865f21 Mon Sep 17 00:00:00 2001
From: SophieS9 <sophie.shaw@wales.nhs.uk>
Date: Wed, 10 Dec 2025 13:25:46 +0000
Subject: [PATCH 1/3] Containerise the repo

---
 .github/workflows/build_container.yml | 61 +++++++++++++++++++++++++++
 Containerfile                         | 10 +++++
 2 files changed, 71 insertions(+)
 create mode 100644 .github/workflows/build_container.yml
 create mode 100644 Containerfile

diff --git a/.github/workflows/build_container.yml b/.github/workflows/build_container.yml
new file mode 100644
index 0000000..a823f38
--- /dev/null
+++ b/.github/workflows/build_container.yml
@@ -0,0 +1,61 @@
+name: Build Image using Containerfile
+on: 
+  push:
+    branches:
+      - 'development'
+    tags:
+
+  pull_request:
+    types: 
+      - opened
+      - synchronize
+    branches:
+      - 'development'
+
+permissions:
+  packages: write
+  contents: read
+
+jobs:
+  build:
+    name: Build image
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Determine tags
+      shell: bash
+      env:
+        REF_TYPE: ${{ github.ref_type }}
+        SHA: ${{ github.sha }}
+        EVENT_NAME: ${{ github.event_name }}
+      run: |
+        if [[ "${EVENT_NAME}" == "pull_request" ]]; then
+          echo "BASE_TAGS=${SHA}" | tee -a "${GITHUB_ENV}"
+        elif [[ "${REF_TYPE}" == "tag" ]]; then 
+          echo "BASE_TAGS=latest ${GITHUB_REF#refs/*/} ${SHA}" | tee -a "${GITHUB_ENV}"
+        elif [[ "${REF_TYPE}" == "branch" ]]; then
+          echo "BASE_TAGS=${GITHUB_REF#refs/*/} ${SHA}" | tee -a "${GITHUB_ENV}"
+        else
+          echo "BASE_TAGS=${SHA}" | tee -a "${GITHUB_ENV}"
+        fi
+
+    - name: Buildah Action
+      id: build_image
+      uses: redhat-actions/buildah-build@v2
+      with:
+        image: CoverageCalculatorPy
+        tags: ${{ env.BASE_TAGS }}
+        containerfiles: |
+          ./Containerfile
+
+    - name: Push to GHCR
+      uses: redhat-actions/push-to-registry@v2
+      if: github.event_name != 'pull_request'
+      with:
+        image: ${{ steps.build_image.outputs.image }}
+        tags: ${{ steps.build_image.outputs.tags }}
+        registry: ghcr.io/awgl
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
diff --git a/Containerfile b/Containerfile
new file mode 100644
index 0000000..f13ec69
--- /dev/null
+++ b/Containerfile
@@ -0,0 +1,10 @@
+FROM docker.io/python:3.11
+
+# Copy script into folder
+COPY CoverageCalculatorPy.py ./
+
+RUN chmod +x CoverageCalculatorPy.py
+
+# Install pytabix
+RUN  pip install pytabix==0.1
+

From d5b9830d602dac4a2ef7a4ae627c5e0e17516cdf Mon Sep 17 00:00:00 2001
From: SophieS9 <sophie.shaw@wales.nhs.uk>
Date: Fri, 12 Dec 2025 13:12:06 +0000
Subject: [PATCH 2/3] Put scripts in a nicer place

---
 Containerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Containerfile b/Containerfile
index f13ec69..783e31f 100644
--- a/Containerfile
+++ b/Containerfile
@@ -1,9 +1,9 @@
 FROM docker.io/python:3.11
 
 # Copy script into folder
-COPY CoverageCalculatorPy.py ./
+COPY CoverageCalculatorPy.py /usr/bin/
 
-RUN chmod +x CoverageCalculatorPy.py
+RUN chmod +x /usr/bin/CoverageCalculatorPy.py
 
 # Install pytabix
 RUN  pip install pytabix==0.1

From 145cd8a465af06b1e90039c39bf86f78bd1a65f6 Mon Sep 17 00:00:00 2001
From: SophieS9 <sophie.shaw@wales.nhs.uk>
Date: Wed, 31 Dec 2025 13:09:22 +0000
Subject: [PATCH 3/3] Add singularity container

---
 env/CoverageCalculatorPy.def | 15 +++++++++++++++
 env/CoverageCalculatorPy.yml |  6 ++----
 2 files changed, 17 insertions(+), 4 deletions(-)
 create mode 100644 env/CoverageCalculatorPy.def

diff --git a/env/CoverageCalculatorPy.def b/env/CoverageCalculatorPy.def
new file mode 100644
index 0000000..d742da7
--- /dev/null
+++ b/env/CoverageCalculatorPy.def
@@ -0,0 +1,15 @@
+Bootstrap: docker
+From: python:3.11
+
+%files
+    ../CoverageCalculatorPy.py /usr/bin/CoverageCalculatorPy.py
+
+%post
+    # Make script executable
+    chmod +x /usr/bin/CoverageCalculatorPy.py
+    
+    # Install pytabix
+    pip install pytabix==0.1
+
+%runscript
+    exec "$@"
diff --git a/env/CoverageCalculatorPy.yml b/env/CoverageCalculatorPy.yml
index adc30e8..b3139eb 100644
--- a/env/CoverageCalculatorPy.yml
+++ b/env/CoverageCalculatorPy.yml
@@ -4,8 +4,6 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - python=3.6.7
-  - zlib=1.2.11
-  - pip:
-    - pytabix==0.1
+  - python=3.11
+  - pytabix=0.1