Add multi-platform SPAdes container support with pigz

.dockerignore

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+.git
+.github
+docs
+.DS_Store
+**/__pycache__/
+**/*.py[cod]
+/bin/
+/build*/
+/spades_test/
+*.tar.gz

.github/workflows/docker.yml

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+name: SPAdes container tests
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - master
+      - main
+      - next
+    tags:
+      - '*'
+    paths-ignore:
+      - 'docs/**'
+      - 'mkdocs.yml'
+  pull_request:
+    paths-ignore:
+      - 'docs/**'
+      - 'mkdocs.yml'
+
+permissions:
+  contents: read
+
+concurrency:
+  group: container-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  container:
+    name: Container (${{ matrix.platform }})
+    runs-on: ${{ matrix.runner }}
+    timeout-minutes: 120
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - runner: ubuntu-24.04
+            platform: linux/amd64
+            architecture: amd64
+          - runner: ubuntu-24.04-arm
+            platform: linux/arm64
+            architecture: arm64
+
+    steps:
+      - name: Check out SPAdes
+        uses: actions/checkout@v7
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v4
+
+      - name: Build container
+        uses: docker/build-push-action@v7
+        with:
+          context: .
+          platforms: ${{ matrix.platform }}
+          load: true
+          push: false
+          tags: spades:ci-${{ matrix.architecture }}
+          cache-from: type=gha,scope=spades-container-${{ matrix.architecture }}
+          cache-to: type=gha,mode=max,scope=spades-container-${{ matrix.architecture }}
+
+      - name: Check runtime environment
+        env:
+          IMAGE_TAG: spades:ci-${{ matrix.architecture }}
+        run: |
+          set -euo pipefail
+
+          expected_version="$(tr -d '\n' < VERSION)"
+          actual_version="$(docker run --rm "${IMAGE_TAG}" spades.py --version)"
+          grep -F "${expected_version}" <<< "${actual_version}"
+
+          docker run --rm "${IMAGE_TAG}" bash -euc '
+            test "$(id -u)" -ne 0
+            touch /work/write-test
+            rm /work/write-test
+            command -v spades.py
+            command -v pigz
+            ! command -v cmake
+            ! command -v g++
+            pigz --version
+          '
+
+      - name: Run SPAdes smoke test
+        env:
+          IMAGE_TAG: spades:ci-${{ matrix.architecture }}
+        run: |
+          docker run --rm "${IMAGE_TAG}" bash -euc '
+            spades.py -t 4 --test
+            grep -F "Compressing corrected reads (with pigz)" spades_test/spades.log
+          '

Dockerfile

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+FROM ubuntu:24.04 AS builder
+
+ARG BUILD_JOBS=8
+ARG DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update \
+    && apt-get install --yes --no-install-recommends \
+        build-essential \
+        cmake \
+        libbz2-dev \
+        python3 \
+        zlib1g-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /src
+COPY . .
+
+RUN PREFIX=/opt/spades ./spades_compile.sh \
+        -j "${BUILD_JOBS}" \
+        -DSPADES_ENABLE_PROJECTS=release \
+        -DSPADES_USE_NCBISDK=ON
+
+
+FROM ubuntu:24.04
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+LABEL org.opencontainers.image.title="SPAdes" \
+      org.opencontainers.image.description="Genome assembler for isolate, single-cell, metagenomic, and transcriptomic sequencing data" \
+      org.opencontainers.image.url="https://ablab.github.io/spades/" \
+      org.opencontainers.image.source="https://github.com/ablab/spades" \
+      org.opencontainers.image.licenses="GPL-2.0-only"
+
+RUN apt-get update \
+    && apt-get install --yes --no-install-recommends \
+        ca-certificates \
+        libbz2-1.0 \
+        libgomp1 \
+        pigz \
+        python3 \
+        zlib1g \
+    && groupadd --gid 1000 spades \
+    && useradd --uid 1000 --gid spades --create-home --shell /bin/bash spades \
+    && install --directory --owner spades --group spades /work \
+    && rm -rf /var/lib/apt/lists/*
+
+COPY --from=builder /opt/spades /opt/spades
+
+ENV PATH="/opt/spades/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
+
+WORKDIR /work
+USER spades
+
+CMD ["/bin/bash"]