Bootstrap: docker
From: ubuntu:bionic
OSversion: 18.04
Include: apt wget

%test
    export PATH="/usr/local/bin:$PATH:/usr/local/conda/bin/"
    . /usr/local/conda/bin/activate
    python --version
    pip --version
    gcc --version
    make --version
    python -c "import numpy"
    mikado --help

%environment
    export PATH="/usr/local/bin:$PATH:/usr/local/conda/bin/"
    # . /usr/local/conda/bin/activate


%post

    ### Install your packages ###
    mkdir /opt/software/
    cd /opt/software/

    apt update -y && apt upgrade -y
    apt install -y build-essential make gcc bzip2 wget git sudo libgtk3-nocsd0
    gcc --version
    make --version

    # Clean up apt
    apt clean

    cd /usr/local/src
    wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
    bash Miniconda3-latest-Linux-x86_64.sh -b -p /usr/local/conda
    export PATH="/usr/local/conda/bin:$PATH"
    . /usr/local/conda/bin/activate
    conda update -y -n base -c defaults conda
    ln -s /usr/local/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh
    conda install -y -c conda-forge pip python==3.6.7
    # Install python requirements
    git clone https://github.com/EI-CoreBioinformatics/mikado.git
    cd mikado
    git log | head -n 1 | cut -f 2 -d " " > MIKADO_COMMIT_HASH
    sed -i 's/;.*//' requirements.txt
    conda install --update-all -y -c conda-forge -c bioconda -c anaconda --file requirements.txt
    python setup.py bdist_wheel
    pip install dist/*whl

    echo '#!/bin/bash' >> /usr/local/bin/show_commit_hash
    echo 'cd /usr/local/src/mikado' >> /usr/local/bin/show_commit_hash
    echo 'git log | head -n1 | cut -f 2 -d " "' >> /usr/local/bin/show_commit_hash
    chmod 775 /usr/local/bin/show_commit_hash

    # Various dependencies for Daijin
    conda install -y -c bioconda -c anaconda -c conda-forge samtools==1.9 openssl=1.0 prodigal blast diamond==0.9.24 transdecoder==5.5.0

%apprun snakemake
	snakemake "@"

%apprun mikado
	mikado "@"

%apprun daijin
    daijin "@"

%apprun snakemake
	snakemake "@"

%apprun mikado
	mikado "@"

%apprun prodigal
    prodigal "@"

%apprun samtools
    samtools "@"

%apprun diamond
    diamond "@"