SCENIC 转录因子分析 Docker 环境构建

原创

翰佰尔生物

发布于 2026-08-10 14:46:34

1060

在进行转录因子分析当中，构建一个可复用，可集成到流程的分析环境十分重要。下面演示具体的思路：

1、以mambaforge:24.1.2-0为基础镜像，通过mamba安装对应版本的Python环境和R环境

2、安装pyscenic、seurat等关键包。

3、默认激活安装的环境。

以下是具体的步骤：

1、编写Dockerfile

# vim Dockerfile
FROM quay.io/condaforge/mambaforge:24.1.2-0
ENV CURL_CA_BUNDLE=/etc/ssl/certs/ca-certificates.crt
ENV CONDA_REMOTE_CONNECT_TIMEOUT=3600
ENV CONDA_REMOTE_READ_TIMEOUT=3600
ENV CONDA_REMOTE_MAX_RETRIES=10
ENV CONDA_REMOTE_BACKOFF_FACTOR=2
RUN apt-get update && \
    apt-get install -y --no-install-recommends \
        libhdf5-dev && \
    apt-get clean && \
    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
RUN mamba create -n pyscenic -c bioconda -c conda-forge -y \
  python=3.8 \
  pyscenic=0.12.1 \
  loompy \
  cytoolz \
  numpy \
  scanpy \
  r-base \
  r-tidyverse \
  r-seurat=4.3.0 \
  r-plotly \
  r-kernsmooth \
  r-rcolorbrewer \
  r-pheatmap \
  r-data.table \
  r-devtools \
  bioconductor-aucell \
  bioconductor-biocparallel \
  bioconductor-viper \
  bioconductor-summarizedexperiment \
  bioconductor-dorothea \
  bioconductor-complexheatmap \
  bioconductor-rcistarget && \
  mamba clean -afy
RUN conda run -n pyscenic R -e "devtools::install_github('aertslab/SCopeLoomR', upgrade='never'); \
          devtools::install_github('aertslab/SCENIC', upgrade='never')"
RUN rm -rf /tmp/Rtmp* /root/.cache /root/.local/share/Trash /opt/conda/envs/pyscenic/.git && \
    conda clean -afy && \
    find /opt/conda -type d -name __pycache__ -prune -exec rm -rf {} + 2>/dev/null || true && \
    find /opt/conda -type f -name "*.pyc" -delete && \
    echo 'conda activate pyscenic' >> /root/.bashrc
CMD ["bash"]

2、执行构建命令