pipeline-container-docker-demo01.md

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FROM condaforge/mambaforge
MAINTAINER liubo (liubo4@genomics.com)

#  conda configure
RUN conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/ &&\
    conda config --add channels defaults &&\
    conda config --add channels bioconda &&\
    # install python
    conda install python=3.9 pandas numpy pyvcf3 pyfaidx pysam pyyaml openpyxl xlrd scikit-allel scikit-learn matplotlib seaborn joblib tqdm -y &&\
    # install vep=110 & perl library
    conda install -c bioconda ensembl-vep==110 -y &&\
    conda install perl-Excel-Writer-XLSX perl-Spreadsheet-XLSX perl-Spreadsheet-ParseExcel -y &&\
    perl -MCPAN -e "install Spreadsheet::XLSX" &&\
    conda update -c conda-forge perl-compress-raw-zlib -y && \
    # install R & library
    conda install -c conda-forge r-base && r-ggplot2 -y
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