Add github action to build docker images

.github/workflows/docker.yml

@@ -0,0 +1,51 @@
+name: Create and publish a Docker image
+
+on:
+  push:
+    branches:
+      - "master"
+    tags:
+      - 'v*'
+  workflow_dispatch:
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        with:
+          context: .
+          platforms: linux/amd64,linux/arm64
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

Dockerfile

@@ -1,37 +1,55 @@
-FROM debian:stable-slim as foldseek-builder
-
-RUN apt-get update && apt-get upgrade -y && apt-get install -y \
-    build-essential cmake xxd git zlib1g-dev libbz2-dev \
- && rm -rf /var/lib/apt/lists/*
+ARG APP=foldseek
+FROM --platform=$BUILDPLATFORM debian:stable-slim as builder
+ARG TARGETARCH
+ARG APP
+
+RUN dpkg --add-architecture $TARGETARCH \
+    && apt-get update \
+    && apt-get install -y \
+      build-essential cmake xxd git \
+      zlib1g-dev libbz2-dev libatomic1 \
+      crossbuild-essential-$TARGETARCH zlib1g-dev:$TARGETARCH libbz2-dev:$TARGETARCH \
+    && rm -rf /var/lib/apt/lists/*
 
-WORKDIR /opt/foldseek
+WORKDIR /opt/build
 ADD . .
 
-RUN mkdir -p build_sse/bin && mkdir -p build_avx/bin
-
-WORKDIR /opt/foldseek/build_sse
-RUN cmake -DHAVE_SSE4_1=1 -DHAVE_MPI=0 -DHAVE_TESTS=0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=. ..; \
-    make -j $(nproc --all) && make install;
-
-WORKDIR /opt/foldseek/build_avx
-RUN cmake -DHAVE_AVX2=1 -DHAVE_MPI=0 -DHAVE_TESTS=0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=. ..; \
-    make -j $(nproc --all) && make install;
+RUN if [ "$TARGETARCH" = "arm64" ]; then \
+      mkdir -p build_$TARGETARCH/src; \
+      cd /opt/build/build_$TARGETARCH; \
+      CC=aarch64-linux-gnu-gcc CXX=aarch64-linux-gnu-g++ cmake -DHAVE_ARM8=1 -DHAVE_MPI=0 -DHAVE_TESTS=0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=. ..; \
+      make -j $(nproc --all); \
+      mv src/${APP} /opt/build/${APP}_arch; \
+      touch /opt/build/${APP}_sse2 /opt/build/${APP}_sse41 /opt/build/${APP}_avx2; \
+    else \
+      mkdir -p build_sse2/src && mkdir -p build_sse41/src && mkdir -p build_avx2/src; \
+      cd /opt/build/build_sse2; \
+      cmake -DHAVE_SSE2=1 -DHAVE_MPI=0 -DHAVE_TESTS=0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=. ..; \
+      make -j $(nproc --all); \
+      mv src/${APP} /opt/build/${APP}_sse2; \
+      cd /opt/build/build_sse41; \
+      cmake -DHAVE_SSE4_1=1 -DHAVE_MPI=0 -DHAVE_TESTS=0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=. ..; \
+      make -j $(nproc --all); \
+      mv src/${APP} /opt/build/${APP}_sse41; \
+      cd /opt/build/build_avx2; \
+      cmake -DHAVE_AVX2=1 -DHAVE_MPI=0 -DHAVE_TESTS=0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=. ..; \
+      make -j $(nproc --all); \
+      mv src/${APP} /opt/build/${APP}_avx2; \
+      touch /opt/build/${APP}_arch; \
+    fi
 
 FROM debian:stable-slim
-MAINTAINER Martin Steinegger <[email protected]>
+MAINTAINER Milot Mirdita <[email protected]>
+ARG APP
 
-RUN apt-get update && apt-get upgrade -y && apt-get install -y \
-     gawk bash grep wget libstdc++6 libgomp1 zlib1g libbz2-1.0 \
+RUN apt-get update && apt-get install -y \
+      gawk bash grep libstdc++6 libgomp1 libatomic1 zlib1g libbz2-1.0 wget tar \
     && rm -rf /var/lib/apt/lists/*
 
-COPY --from=foldseek-builder /opt/foldseek/build_sse/bin/foldseek /usr/local/bin/foldseek_sse42
-COPY --from=foldseek-builder /opt/foldseek/build_avx/bin/foldseek /usr/local/bin/foldseek_avx2
-RUN echo '#!/bin/bash\n\
-if $(grep -q -E "^flags.+avx2" /proc/cpuinfo); then\n\
-    exec /usr/local/bin/foldseek_avx2 "$@"\n\
-else\n\
-    exec /usr/local/bin/foldseek_sse42 "$@"\n\
-fi' > /usr/local/bin/foldseek
-RUN chmod +x /usr/local/bin/foldseek
-
-ENTRYPOINT ["/usr/local/bin/foldseek"]
+COPY --from=builder /opt/build/${APP}_arch /opt/build/${APP}_sse2 /opt/build/${APP}_sse41 /opt/build/${APP}_avx2 /usr/local/bin/
+ADD util/${APP}_wrapper.sh /usr/local/bin/${APP}
+RUN if [ "$TARGETARCH" = "arm64" ]; then mv -f /opt/build/${APP}_arch /usr/local/bin/${APP}; fi
+
+ENV APP=$APP
+ENTRYPOINT /usr/local/bin/${APP}
+

util/foldseek_wrapper.sh

@@ -0,0 +1,13 @@
+#!/bin/sh
+FLAGS="$(grep -m 1 '^flags' /proc/cpuinfo)"
+case "${FLAGS}" in
+  *avx2*)
+    exec /usr/local/bin/foldseek_avx2 "$@"
+    ;;
+  *sse4_1*)
+    exec /usr/local/bin/foldseek_sse41 "$@"
+    ;;
+  *)
+    exec /usr/local/bin/foldseek_sse2 "$@"
+    ;;
+esac