44 lines
1.8 KiB
Docker
44 lines
1.8 KiB
Docker
# bioflow-rnaseq —— RNA-seq 主链(qc/align/quant/de/enrich/fgsea/wgcna)
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# 源环境: rnaseq (Python 3.11.15); 方法: docs/bioflow_image_build_playbook.md
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# 每镜像=单一 conda 环境, 仅 root, 无 /home/xzq, 无 conda 本体; 工具一律 PATH 裸命令。
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ARG BASE_IMAGE=ubuntu:24.04
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FROM ${BASE_IMAGE} AS unpack
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ARG ENV_TAR
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ARG EXTRAS_TAR
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COPY ${ENV_TAR} /tmp/env.tar.gz
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RUN mkdir -p /opt/conda && \
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(tar --ignore-zeros -xzf /tmp/env.tar.gz -C /opt/conda || true) && \
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rm -f /tmp/env.tar.gz && \
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test -x /opt/conda/bin/python
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# 先 PATH 再 conda-unpack(其 shebang 为 /usr/bin/env python)
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ENV PATH=/opt/conda/bin:$PATH
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ENV LANG=C.UTF-8
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# 先 conda-unpack(其文件清单含 bin/activate 等前缀重写目标, 不能先删),
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# 再删除 conda-pack 注入的 conda 桩(镜像红线: 无 conda 可执行文件)
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RUN conda-unpack && \
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rm -f /opt/conda/bin/conda /opt/conda/bin/activate /opt/conda/bin/deactivate
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# 宿主外部软链修复: 14 个 STAR* -> mamba env bin(conda-pack 原样打包为断链)
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# extras tar = biolabx-bioinfo-missing/bin/STAR* 的打包; 镜像内解包到 /opt/star-bin 后重指。
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COPY ${EXTRAS_TAR} /tmp/extras.tar.gz
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RUN mkdir -p /opt/star-bin && \
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tar -xzf /tmp/extras.tar.gz -C /opt/star-bin && \
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rm -f /tmp/extras.tar.gz && \
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for s in /opt/conda/bin/STAR /opt/conda/bin/STARlong; do \
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ln -sfn /opt/star-bin/$(basename "$s") "$s"; \
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done && \
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for s in /opt/conda/bin/STAR-*; do \
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ln -sfn /opt/star-bin/$(basename "$s") "$s"; \
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done && \
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test -x /opt/conda/bin/STAR
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FROM ${BASE_IMAGE}
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COPY --from=unpack /opt/conda /opt/conda
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COPY --from=unpack /opt/star-bin /opt/star-bin
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ENV PATH=/opt/conda/bin:$PATH
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# STAR 系 mamba 环境二进制, 依赖 libhts.so.3/libgomp.so.1(镜像 /opt/conda/lib 已含)
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ENV LD_LIBRARY_PATH=/opt/conda/lib
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ENV LANG=C.UTF-8
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