migrated to action for workflow

Author: poquirion

Diff for: .docker_login

@@ -0,0 +1,55 @@
+---
+name: build-image
+
+on:
+  push:
+    branches:
+    tags:
+      - 'v*'
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    env:
+      GH_REPO: poquirion/ncov-tools
+    steps:
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+      - name: Login to DockerHub
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      - name: Build on all branch
+        id: alpha
+        uses: docker/build-push-action@v2
+        with:
+          push: true
+          tags: ${{ env.GH_REPO }}:alpha
+          cache-from: type=registry,ref=${{ env.GH_REPO }}:alpha
+          cache-to: type=inline
+      -
+        name: Docker meta
+        id: docker_meta
+        uses: crazy-max/ghaction-docker-meta@v1
+        with:
+          images: ${{ env.GH_REPO }} # list of Docker images to use as base name for tags
+          tag-sha: true # add git short SHA as Docker tag
+      - name: push latest
+        if: ${{ github.ref == 'ref/head/master' }}
+        id: latest
+        uses: docker/build-push-action@v2
+        with:
+          push: true
+          tags: ${{ env.GH_REPO }}:latest
+          cache-from: type=registry,ref=${{ env.GH_REPO }}:alpha
+          cache-to: type=inline
+      - name: push tag
+        if: contains(github.ref, 'tags/v')
+        id: tag
+        uses: docker/build-push-action@v2
+        with:
+          push: true
+          cache-from: type=registry,ref=${{ env.GH_REPO }}:alpha
+          cache-to: type=inline
+          tags: ${{ steps.docker_meta.outputs.tags }}
+          labels: ${{ steps.docker_meta.outputs.labels }}

Diff for: .github/workflows/publish_image.yaml

@@ -8,12 +8,10 @@ RUN conda install pycryptosat \
  && conda config --set channel_priority strict
 
 ENV NCOV ncov-qc
-# make that two steps (base and then tools)
 ADD workflow/envs/environment.yml environment.yml
-ADD parser parser
 RUN conda env create --name $NCOV -f environment.yml \
     && rm -rf /opt/conda/pkgs/
-RUN /opt/conda/envs/$NCOV/bin/pip install ./parser
+# make sure that container is not polluted by ~/.local install
 ENV PYTHONNOUSERSITE=1
 RUN mkdir -p /app/workdir
 ADD workflow /app
@@ -23,7 +21,7 @@ WORKDIR /app/workdir
 RUN  mkdir -p /.singularity.d/env \
   && echo ". /etc/profile.d/conda.sh" >> /etc/bash.bashrc \
   && echo ". /etc/profile.d/conda.sh" >>  /.singularity.d/env/999-conda.sh \
-  && echo "conda activate $NCOV" >>  /etc/bash.bashrc \
-  && echo "conda activate $NCOV" >> /.singularity.d/env/999-conda.sh \
+  && echo "conda activate $NCOV 2>/dev/null" >>  /etc/bash.bashrc \
+  && echo "conda activate $NCOV 2>/dev/null" >> /.singularity.d/env/999-conda.sh \
   && rm /root/.bashrc && rm /bin/sh && ln -s /bin/bash /bin/sh
-#docker build --tag ncov-tools .  &&  singularity build ../.snakemake/singularity/7f0a6cf10df7320052c57c5468fcf292.simg docker-daemon://ncov-tools:latest
+#docker build --tag ncov-tools .  &&  singularity build ncov_tools.simg docker-daemon://ncov-tools:latest