albicans2021/trim_galore repository overview

############################
# Builder: build wheels (src→wheel)
############################
FROM python:3.11-bookworm AS wheels

ARG CUTADAPT_VERSION=4.9

RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
    --mount=type=cache,target=/var/lib/apt,sharing=locked \
    set -eux; \
    apt-get update; \
    apt-get -y --no-install-recommends dist-upgrade; \
    apt-get -o APT::Keep-Downloaded-Packages=false \
            -o Dir::Cache::Archives=/tmp \
            install -y --no-install-recommends build-essential python3-dev cython3; \
    rm -rf /var/lib/apt/lists/* /var/cache/apt/* /tmp/*

# setuptools のCVE回避（>=78.1.1）
RUN python -m pip install --upgrade --no-cache-dir pip wheel "setuptools>=78.1.1"

# 依存もまとめてwheel化
RUN pip wheel --no-cache-dir --wheel-dir /wheels "cutadapt==${CUTADAPT_VERSION}"

############################
# Runtime
############################
FROM python:3.11-slim-bookworm

LABEL maintainer="albicans" \
      org.opencontainers.image.title="trim_galore" \
      org.opencontainers.image.version="2.3" \
      org.opencontainers.image.description="Trim Galore + (optional) FastQC + Cutadapt runtime" \
      org.opencontainers.image.source="https://hub.docker.com/r/albicans2021/trim_galore"

# --- Build args / options ---
ARG UID=1000
ARG GID=1000
ARG CUTADAPT_VERSION=4.9

# FastQC を含めるか（true/false）
ARG WITH_FASTQC=true
# FastQC 0.12.1（任意で変更）
ARG FASTQC_VER="0.12.1"
ARG FASTQC_URL="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v${FASTQC_VER}.zip"
# SHA256 を指定したい場合に渡す（未設定なら検証スキップ）
ARG FASTQC_SHA256=""

ENV PIP_NO_CACHE_DIR=1 \
    PYTHONDONTWRITEBYTECODE=1 \
    PYTHONUNBUFFERED=1 \
    LC_ALL=C.UTF-8 LANG=C.UTF-8 \
    TZ=Asia/Tokyo \
    PATH="/usr/local/FastQC:${PATH}"

# --- OS セキュリティアップデート & 最小導入 ---
RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
    --mount=type=cache,target=/var/lib/apt,sharing=locked \
    set -eux; \
    apt-get update; \
    apt-get -y --no-install-recommends dist-upgrade; \
    apt-get -o APT::Keep-Downloaded-Packages=false \
            -o Dir::Cache::Archives=/tmp \
            install -y --no-install-recommends ca-certificates; \
    rm -rf /var/lib/apt/lists/* /var/cache/apt/* /tmp/*

# Python toolchain更新（setuptoolsのCVE回避、ランタイム側にも常駐）
RUN python -m pip install --upgrade --no-cache-dir pip wheel "setuptools>=78.1.1"

# cutadapt を wheels からオフライン導入
COPY --from=wheels /wheels /wheels
RUN pip install --no-index --find-links=/wheels "cutadapt==${CUTADAPT_VERSION}" && rm -rf /wheels

# --- Trim Galore（Perlスクリプト） ---
COPY ./tools/TrimGalore-0.6.10/trim_galore /usr/local/bin/trim_galore
RUN chmod +x /usr/local/bin/trim_galore

# --- FastQC（任意; WITH_FASTQC=true の場合のみ導入） ---
# zip は ADD で取得（curl/unzip不要）
ADD ${FASTQC_URL} /tmp/fastqc.zip

# 解凍は Python の zipfile を使用。FastQC動作用の Perlモジュール と Java を条件導入
RUN set -eux; \
    if [ "${WITH_FASTQC}" = "true" ]; then \
      if [ -n "${FASTQC_SHA256}" ]; then \
        echo "${FASTQC_SHA256}  /tmp/fastqc.zip" | sha256sum -c -; \
      else \
        echo "FASTQC_SHA256 not set; skipping checksum verification"; \
      fi; \
      python -c "import zipfile,os; z=zipfile.ZipFile('/tmp/fastqc.zip'); z.extractall('/usr/local'); z.close(); os.remove('/tmp/fastqc.zip')"; \
      chmod +x /usr/local/FastQC/fastqc; \
      ln -sf /usr/local/FastQC/fastqc /usr/bin/fastqc; \
      # ★ FastQCのPerl依存（FindBin等）は perl-modules-5.36 に含まれる
      apt-get update; \
      apt-get -y --no-install-recommends install perl-modules-5.36 openjdk-17-jre-headless; \
      apt-get clean; rm -rf /var/lib/apt/lists/*; \
    else \
      rm -f /tmp/fastqc.zip || true; \
    fi

# --- 使わないパッケージのパージ（存在すれば） ---
RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
    --mount=type=cache,target=/var/lib/apt,sharing=locked \
    set -eux; \
    apt-get update; \
    DEBIAN_FRONTEND=noninteractive apt-get -y purge --auto-remove --allow-remove-essential \
      tar sqlite3 cups gnupg2 || true; \
    apt-get -y autoremove --purge || true; \
    apt-get clean; \
    rm -rf /var/lib/apt/lists/* /var/cache/apt/* /tmp/*

# --- Non-root user ---
RUN set -eux; groupadd -g "${GID}" main; useradd -m -s /bin/bash -u "${UID}" -g "${GID}" main
USER main
WORKDIR /home/main

# --- Healthcheck（FastQC有無を考慮） ---
HEALTHCHECK --interval=1m --timeout=10s --start-period=20s --retries=3 \
  CMD bash -lc 'trim_galore --version >/dev/null 2>&1 && { [ "${WITH_FASTQC}" = "true" ] && fastqc --version >/dev/null 2>&1 || true; } || exit 1'

CMD ["trim_galore", "--help"]

# -------------- Builder Stage --------------
FROM ubuntu:22.04 AS builder

LABEL maintainer="albicans" \
      image_name="albicans2021/trim_galore" \
      version="1.5"

# 必要なパッケージをインストール（不要な依存関係は入れない）
RUN apt-get update && apt-get install -y --no-install-recommends \
        perl unzip default-jre #python3 python3-pip \
    && pip install cutadapt \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*

# FastQC のインストール
COPY ./tools/fastqc_v0.11.9.zip /usr/local
RUN unzip /usr/local/fastqc_v0.11.9.zip -d /usr/local \
    && rm /usr/local/fastqc_v0.11.9.zip \
    && chmod +x /usr/local/FastQC/fastqc

# Trim Galore のインストール
COPY ./tools/TrimGalore-0.6.10/trim_galore /usr/local/bin
RUN chmod +x /usr/local/bin/trim_galore

# -------------- Runtime Stage --------------
FROM python:3.9-slim-buster AS runtime

# 必要なランタイムパッケージのみをインストール
RUN apt-get update && apt-get install -y --no-install-recommends \
        perl default-jre \
    && pip install cutadapt \
    && ln -fs /usr/share/zoneinfo/Asia/Tokyo /etc/localtime \
    && echo "Asia/Tokyo" > /etc/timezone \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*

# FastQC & Trim Galore のみをコピー（Python はランタイムでインストール済み）
COPY --from=builder /usr/local/FastQC /usr/local/FastQC
COPY --from=builder /usr/local/bin/trim_galore /usr/local/bin/trim_galore
#COPY --from=builder /usr/bin/python3 /usr/bin/python3

# FastQC のシンボリックリンクを作成
RUN ln -s /usr/local/FastQC/fastqc /usr/bin/fastqc

# ユーザー作成
RUN groupadd -g 1000 main && useradd -m -s /bin/bash -u 1000 -g 1000 main

# エントリーポイントを設定
USER main
WORKDIR /home/main