Merge pull request #59 from metagenlab/container

Add docker container

.github/workflows/docker-publish.yml

@@ -0,0 +1,78 @@
+name: Publish Docker image
+
+on:
+  pull_request:
+    paths:
+      - "Dockerfile"
+      - "env.yaml"
+      - ".github/workflows/docker-publish.yml"
+      - "zamp/**"
+      - "setup.py"
+      - "!docs/**"
+      - "!*.md"
+      - "!LICENSE"
+  push:
+    branches: [main]
+    paths:
+      - "Dockerfile"
+      - "env.yaml"
+      - ".github/workflows/docker-publish.yml"
+      - "zamp/**"
+      - "setup.py"
+      - "!docs/**"
+      - "!*.md"
+      - "!LICENSE"
+
+  release:
+    types: [published]
+
+jobs:
+  push_to_registry:
+    if: github.repository == 'metagenlab/zAMP'
+    name: Build + Push Docker image
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v4
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Login to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ vars.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Push dev image
+        uses: docker/build-push-action@v6
+        if: github.event_name == 'push'
+        with:
+          platforms: linux/amd64,linux/arm64
+          push: true
+          tags: |
+            ghcr.io/metagenlab/zamp:dev
+            metagenlab/zamp:dev
+
+      - name: Push release image
+        uses: docker/build-push-action@v6
+        if: github.event_name == 'release'
+        with:
+          platforms: linux/amd64,linux/arm64
+          push: true
+          tags: |
+            ghcr.io/metagenlab/zamp:${{ github.event.release.tag_name }}
+            ghcr.io/metagenlab/zamp:latest
+            metagenlab/zamp:${{ github.event.release.tag_name }}
+            metagenlab/zamp:latest

Dockerfile

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+FROM mambaorg/micromamba
+LABEL org.opencontainers.image.source=https://github.com/metagenlab/zAMP
+LABEL org.opencontainers.image.description="Snakemake pipeline for convenient amplicon metagenomics anlysis"
+LABEL org.opencontainers.image.licenses=MIT
+ENV LANG=C.UTF-8 
+ENV SHELL=/bin/bash
+
+USER root
+ENV APT_PKGS="procps ca-certificates"
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends ${APT_PKGS} \
+    && apt-get clean \
+    && rm -rf /var/lib/apt /var/lib/dpkg /var/lib/cache /var/lib/log
+USER $MAMBA_USER
+
+COPY --chown=$MAMBA_USER:$MAMBA_USER . /pkg
+RUN micromamba config set extract_threads 1 && \
+    micromamba install -n base -y -f /pkg/env.yaml && \
+    micromamba clean -afy 
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+RUN pip install /pkg --no-deps --no-build-isolation --no-cache-dir -vvv
+ENV PATH="/opt/conda/bin:$PATH" XDG_CACHE_HOME=/tmp

env.yaml

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+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - apptainer =1.3.2
+  - python =3.12
+  - pip
+  - Click =8.1.3
+  - metasnek =0.0.8
+  - snaketool-utils =0.0.5
+  - snakemake-minimal =8.24
+  - snakemake-executor-plugin-slurm =0.11.2
+  - attrmap =0.0.7
+  - biopython =1.83
+  - pandas =2.2.1
+