# Need a Pathway-tools installer in the same folder.
Bootstrap: docker
From: ubuntu:18.04

%files
    pathway-tools-23.5-linux-64-tier1-install /opt
    metacyc_23.5.padmet /opt

%environment
    export PATH="$PATH:/programs/pathway-tools:"
    export PATH="/opt/conda/bin:${PATH}"
    export LANG="C.UTF-8"

%post
    apt-get -y update && \
    DEBIAN_FRONTEND=noninteractive apt-get install -y \
    curl \
    make \
    wget \
    csh \
    git \
    ncbi-blast+ \
    libxm4 \
    vim \
    r-base \
    python3-dev \
    python3-distutils \
    iputils-ping \
    screen \
    exonerate \
    gnome-terminal ;\
    apt-get clean; \
    apt-get purge ;\
    wget -c https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh ;\
    /bin/bash Miniconda3-latest-Linux-x86_64.sh -bfp /usr/local ;\
    conda update conda ;\
    conda install -c bioconda orthofinder=2.5.4  ;\
    mkdir -p /programs/ /shared/ /home/database/BIOCYC/METACYC/23/ ;\
    cd /opt ;\
    mv metacyc_23.5.padmet /home/database/BIOCYC/METACYC/23/ ;\
    mkdir -p /external/folder ;\
    chmod u+x pathway-tools-23.5-linux-64-tier1-install ;\
    ./pathway-tools-23.5-linux-64-tier1-install --InstallDir /programs/pathway-tools --PTOOLS_LOCAL_PATH /external/folder/ --InstallDesktopShortcuts 0 --mode unattended ;\
    cp -r /external/folder/ptools-local /opt ;\
    rm pathway-tools-23.5-linux-64-tier1-install ;\
    R -e "install.packages('https://cran.r-project.org/src/contrib/Archive/pvclust/pvclust_2.0-0.tar.gz', repos=NULL, type='source', dependencies=TRUE)";\
    R -e "install.packages('ape', dependencies=TRUE)";\
    curl https://bootstrap.pypa.io/get-pip.py | python3 ;\
    pip3 install seaborn scipy lxml rpy2 supervenn tzlocal ;\
    cd /programs ;\
    git clone https://github.com/AuReMe/mpwt.git ;\
    cd mpwt ;\
    python3 setup.py develop ;\
    cd .. ;\
    git clone https://github.com/AuReMe/padmet.git ;\
    cd padmet ;\
    python3 setup.py develop ;\
    cd .. ;\
    git clone https://github.com/AuReMe/aucome.git ;\
    cd aucome ;\
    python3 setup.py develop
