Singularity.def

	Bootstrap: docker                                                                                                                                                                    
From: ubuntu:latest                                                                                                                                                                  
                                                                                                                                                                                     
%environment
    source /opt/software/conda/bin/activate /opt/software/conda-env
    export PATH=/opt/software/CAT/CAT_pack/:$PATH
%post
    apt -y update
    apt -y install -y build-essential wget git automake zlib1g zlib1g-dev pkg-config curl

    mkdir -p /opt/software && cd /opt/software

    git clone https://github.com/dutilh/CAT

    curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
    sh ./Miniconda3-latest-Linux-x86_64.sh -p /opt/software/conda -b
       
    /opt/software/conda/bin/conda config --add channels bioconda
    /opt/software/conda/bin/conda config --add channels conda-forge

    /opt/software/conda/bin/conda create -p /opt/software/conda-env -y  spades bbmap quast emboss minimap2 samtools qualimap hisat2 stringtie metabat2 barrnap diamond blast checkm-genome cat busco=5.7 
    /opt/software/conda/bin/conda clean --all --yes