add qctool container

.github/workflows/docker-publish-qctool.yml

@@ -0,0 +1,60 @@
+name: Docker
+
+on:
+  push:
+    branches: [ "main" ]
+    # Publish semver tags as releases.
+    tags: [ 'v*.*.*' ]
+  pull_request:
+    branches: [ "main" ]
+
+env:
+  # Use docker.io for Docker Hub if empty
+  REGISTRY: ghcr.io
+  # github.repository as <account>/<repo>
+  IMAGE_NAME: ${{ github.repository }}/qctool
+  IMAGE_TAG: 2.2.0
+
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Lint Dockerfile
+        uses: hadolint/[email protected]
+        with:
+          dockerfile: qctool/Dockerfile
+
+      # Workaround: https://github.com/docker/build-push-action/issues/461
+      - name: Setup Docker buildx
+        uses: docker/setup-buildx-action@79abd3f86f79a9d68a23c75a09a9a85889262adf
+
+      # Login against a Docker registry except on PR
+      # https://github.com/docker/login-action
+      - name: Log into registry ${{ env.REGISTRY }}
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@28218f9b04b4f3f62068d7b6ce6ca5b26e35336c
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      # Build and push Docker image with Buildx (don't push on PR)
+      # https://github.com/docker/build-push-action
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@ac9327eae2b366085ac7f6a2d02df8aa8ead720a
+        with:
+          context: qctool/
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ env.IMAGE_TAG }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max

README.md

@@ -1,3 +1,3 @@
 # containers
 
-Container recipes used to build images for our bioinformatics/statistical analysis.
+Container recipes that are used to build the images for our bioinformatics/statistical pipelines.

qctool/Dockerfile

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+# hadolint global ignore=SC2086,DL3033,SC1091
+# Dockerfile
+
+# https://hub.docker.com/_/rockylinux
+FROM rockylinux:8
+ENV container docker
+
+WORKDIR "/lib/systemd/system/sysinit.target.wants/"
+RUN (for i in *; do [ $i == \
+systemd-tmpfiles-setup.service ] || rm -f $i; done); \
+rm -f /lib/systemd/system/multi-user.target.wants/*;\
+rm -f /etc/systemd/system/*.wants/*;\
+rm -f /lib/systemd/system/local-fs.target.wants/*; \
+rm -f /lib/systemd/system/sockets.target.wants/*udev*; \
+rm -f /lib/systemd/system/sockets.target.wants/*initctl*; \
+rm -f /lib/systemd/system/basic.target.wants/*;\
+rm -f /lib/systemd/system/anaconda.target.wants/*;
+VOLUME [ "/sys/fs/cgroup" ]
+
+RUN yum -y install wget ca-certificates gcc lapack; yum clean all;
+
+# Install qctool 2
+WORKDIR "/tmp/"
+RUN  wget -q https://www.well.ox.ac.uk/~gav/resources/qctool_v2.2.0-CentOS_Linux7.8.2003-x86_64.tgz \
+&&   tar -xvf qctool_v2.2.0-CentOS_Linux7.8.2003-x86_64.tgz && rm -f qctool_v2.2.0-CentOS_Linux7.8.2003-x86_64.tgz \
+&&   mv qctool_v2.2.0-CentOS\ Linux7.8.2003-x86_64/qctool /usr/local/bin/ && chmod a+rwx /usr/local/bin/qctool \
+&&   rm -rf qctool_v2.2.0-CentOS\ Linux7.8.2003-x86_64
+
+ENV PATH=/usr/local/bin:$PATH
+
+CMD ["/usr/sbin/init"]
+