Dockerfile

FROM continuumio/miniconda3:4.12.0

LABEL \
    author="Shenghui huang" \
    maintainer="Shenghui huang" \
    email="hsh-me@outlook.com" \
    description="Docker Image for ASTK"

# Install system dependencies
# RUN apt update -y && apt install -y libcurl4-openssl-dev libxml2-dev libssl-dev \
#      libreadline-dev build-essential gosu libexpat-dev &&  \
#      apt autoremove -y && apt clean -y && apt purge -y && rm -rf /tmp/* /var/tmp/* && \
#      mkdir -p /home/software/astk /project

RUN apt update -y && \
    apt install -y \
        libcurl4-openssl-dev libxml2-dev libssl-dev \
        libreadline-dev build-essential gosu libexpat-dev \
        ghostscript  zlib1g-dev autoconf automake libtool  \
        libgs-dev \
        libgd-dev \
        libexpat1-dev \
        libhtml-template-compiled-perl \
        libxml-opml-simplegen-perl \
        libxml-libxml-debugging-perl \
        libxslt-dev && \
    apt autoremove -y && \
    apt clean -y && \
    apt purge -y && \
    rm -rf /tmp/* /var/tmp/* && \
    mkdir -p /home/software/astk /project


# install meme-suite perl dependencies
RUN PERL_MM_USE_DEFAULT=1 perl -MCPAN -e 'install Log::Log4perl' && \
    PERL_MM_USE_DEFAULT=1 perl -MCPAN -e 'install HTML::Template' && \
    PERL_MM_USE_DEFAULT=1 perl -MCPAN -e 'install Math::CDF'  

# install meme-suite 
ADD meme-5.4.1.tar.gz /home/software/
RUN cd /home/software/meme-5.4.1 && \ 
    ./configure --prefix=/home/software/meme --enable-build-libxml2 --enable-build-libxslt && \
    make && make install 


# install R packages
RUN conda install -y -c https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge/ --override-channels \
        r-base=4.1.3 r-upsetr=1.4.0  r-argparse=2.1.6 r-ggnewscale=0.4.7 r-tidyverse=1.3.2 \
        r-ggplot2=3.3.6 r-biocmanager=1.30.18 r-usethis=2.1.6 r-ggraph=2.0.6 && \
    Rscript -e "options(BioC_mirror='https://mirrors.tuna.tsinghua.edu.cn/bioconductor');\
        BiocManager::install(c('clusterProfiler', 'org.Mm.eg.db', 'tximport', 'ComplexHeatmap', \
        'org.Hs.eg.db', 'simplifyEnrichment','universalmotif', 'DESeq2', 'ReactomePA'))" 


ENV PATH="${PATH}:/home/software/meme/bin:/home/software/meme/libexec/meme-5.4.1"

COPY docker-entrypoint.sh /usr/local/bin/docker-entrypoint.sh
COPY setup.py /home/software/astk/setup.py
COPY astk /home/software/astk/astk

# Install astk
RUN python -m pip install --upgrade pip -i https://mirrors.bfsu.edu.cn/pypi/web/simple && \
    pip install -e /home/software/astk/ -i https://mirrors.bfsu.edu.cn/pypi/web/simple && \
    chmod a+x /usr/local/bin/docker-entrypoint.sh

WORKDIR /project

ENTRYPOINT ["/usr/local/bin/docker-entrypoint.sh"]