Merge pull request #1 from msk-access/msk-access

Msk access

.github/workflows/deploy-pypi.yml

@@ -1,32 +1,31 @@
-name: Publish MultiQC to PyPI
-on:
-  release:
-    types: [published]
-
-jobs:
-  build-n-publish:
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/checkout@v2
-        name: Check out source-code repository
-
-      - name: Set up Python 3.7
-        uses: actions/setup-python@v1
-        with:
-          python-version: 3.7
-
-      - name: Install python dependencies
-        run: |
-          python -m pip install --upgrade pip setuptools wheel build
-          pip install .
-
-      - name: Build the distribution
-        run: python setup.py sdist bdist_wheel
-
-      - name: Publish MultiQC to PyPI
-        if: github.repository == 'ewels/MultiQC'
-        uses: pypa/gh-action-pypi-publish@master
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_API_TOKEN }}
+# name: Publish MultiQC to PyPI
+# on:
+#   release:
+#     types: [published]
+#
+# jobs:
+#   build-n-publish:
+#     runs-on: ubuntu-latest
+#
+#     steps:
+#       - uses: actions/checkout@v2
+#         name: Check out source-code repository
+#
+#       - name: Set up Python 3.7
+#         uses: actions/setup-python@v1
+#         with:
+#           python-version: 3.7
+#
+#       - name: Install python dependencies
+#         run: |
+#           python -m pip install --upgrade pip setuptools wheel build twine
+#           pip install .
+#
+#       - name: Build the distribution
+#         run: python setup.py sdist bdist_wheel
+#
+#       - name: Publish MultiQC-MSK to PyPI
+#         uses: pypa/gh-action-pypi-publish@master
+#         with:
+#           user: __token__
+#           password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/publish_docker.yml

@@ -0,0 +1,69 @@
+name: Publish Docker image
+on:
+  release:
+    types: [published]
+jobs:
+  push_to_registries:
+    name: Build and publish Docker image
+    runs-on: ubuntu-latest
+    steps:
+      -
+        name: Check out the repo
+        uses: actions/checkout@v2
+      -
+        name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+      -
+        name: Prepare
+        # In this preparation step, a few configurations are made
+        # according to tags that will be used to export the image
+        # for Docker Hub, as well as the name of the image itself
+        id: prep
+        run: |
+          DOCKER_IMAGE=ghcr.io/msk-access/multiqc
+          VERSION=noop
+          if [ "${{ github.event_name }}" = "schedule" ]; then
+            VERSION=nightly
+          elif [[ $GITHUB_REF == refs/tags/* ]]; then
+            VERSION=${GITHUB_REF#refs/tags/}
+          elif [[ $GITHUB_REF == refs/heads/* ]]; then
+            VERSION=$(echo ${GITHUB_REF#refs/heads/} | sed -r 's#/+#-#g')
+          fi
+          TAGS="${DOCKER_IMAGE}:${VERSION}"
+          if [[ $VERSION =~ ^[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}$ ]]; then
+            MINOR=${VERSION%.*}
+            MAJOR=${MINOR%.*}
+            TAGS="$TAGS,${DOCKER_IMAGE}:${MINOR},${DOCKER_IMAGE}:${MAJOR},${DOCKER_IMAGE}:latest"
+          elif [[ $VERSION =~ ^v[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}$ ]]; then
+            VERSION=$(echo ${VERSION#v})
+            TAGS="${DOCKER_IMAGE}:${VERSION}"
+          elif [ "${{ github.event_name }}" = "push" ]; then
+            TAGS="$TAGS,${DOCKER_IMAGE}:sha-${GITHUB_SHA::8}"
+          fi
+          echo ::set-output name=version::${VERSION}
+          echo ::set-output name=tags::${TAGS}
+      -
+        name: Login to GitHub Container Registry
+        #if: github.event_name != 'pull_request'
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.RS_PAT }}
+      - name: Push to GitHub Packages
+        uses: docker/build-push-action@v2
+        with:
+          context: .
+          file: ./Dockerfile
+          registry: ghcr.io
+          push: true
+          tags: ${{ steps.prep.outputs.tags }}
+          build-args: |
+            MULTIQC_VERSION=${{ steps.prep.outputs.version }}
+          labels: |
+            org.opencontainers.image.title=${{ github.event.repository.name }}
+            org.opencontainers.image.description=${{ github.event.repository.description }}
+            org.opencontainers.image.version=${{ steps.prep.outputs.version }}

Dockerfile

@@ -1,19 +1,47 @@
 # Teeny-tiny matplotlib image based on alpine
-FROM czentye/matplotlib-minimal:3.1.2
+FROM python:3.6-slim
 
 LABEL author="Phil Ewels" \
       description="MultiQC" \
       maintainer="phil.ewels@scilifelab.se"
 
-RUN apk add --no-cache bash
+# RUN apk add --no-cache bash gcc gfortran build-base wget freetype-dev libpng-dev openblas-dev
 
 # Add the MultiQC source files to the container
 ADD . /usr/src/multiqc
 WORKDIR /usr/src/multiqc
 
+ENV LC_ALL en_US.utf-8
+ENV LANG en_US.utf-8
+ENV PYTHONIOENCODING utf-8
+ENV LC_ALL=en_US.utf-8
+ENV LANG=en_US.utf-8
+ENV PYTHONIOENCODING=utf-8
+
+RUN apt-get -qq update && \
+    apt-get -q -y upgrade && \
+    apt-get install -y locales
+
+RUN sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/'        /etc/locale.gen \
+ && sed -i -e 's/# pt_BR.UTF-8 UTF-8/pt_BR.UTF-8 UTF-8/' /etc/locale.gen \
+ && locale-gen en_US.utf-8
+
 # Install MultiQC
+RUN pip install --upgrade pip && pip install --no-cache-dir scipy
 RUN python -m pip install .
 
-# Set up entrypoint and cmd for easy docker usage
-ENTRYPOINT [ "multiqc" ]
-CMD [ "." ]
+ENV LC_ALL en_US.utf-8
+ENV LANG en_US.utf-8
+ENV PYTHONIOENCODING utf-8
+ENV LC_ALL=en_US.utf-8
+ENV LANG=en_US.utf-8
+ENV PYTHONIOENCODING=utf-8
+
+CMD ["/bin/bash"]
+
+ENV LC_ALL en_US.utf-8
+ENV LANG en_US.utf-8
+ENV PYTHONIOENCODING utf-8
+ENV LC_ALL=en_US.utf-8
+ENV LANG=en_US.utf-8
+ENV PYTHONIOENCODING=utf-8