sing_final.def

BootStrap: library
From: ubuntu:22.04

%environment
    # set up all essential environment variables
    export PATH="/opt/emu/:/opt/minimap2-2.24_x64-linux/minimap2:/opt/minimap2-2.24_x64-linux/:/opt/miniconda3/bin/:/opt/miniconda3/bin/conda:$PATH"

    # activate conda environment
    source activate base
    conda activate

%post
    # update and install essential dependencies
    apt-get -y update
    apt-get update && apt-get install -y build-essential bzip2 wget git default-jre unzip

    # download, install, and update miniconda3
    wget https://repo.anaconda.com/miniconda/Miniconda3-py37_23.1.0-1-Linux-x86_64.sh
    bash Miniconda3-py37_23.1.0-1-Linux-x86_64.sh -b -f -p /opt/miniconda3/
    rm Miniconda3*sh
    
    # download and install minimap2
    wget https://github.com/lh3/minimap2/releases/download/v2.24/minimap2-2.24_x64-linux.tar.bz2 
    tar -jxvf minimap2-2.24_x64-linux.tar.bz2 
    mv minimap2-2.24_x64-linux /opt/
    export PATH="/opt/miniconda3/bin:/opt/miniconda3/bin/conda:$PATH"
    export PATH="/opt/minimap2-2.24_x64-linux/minimap2:$PATH"
    rm minimap2-2.24_x64-linux.tar.bz2


    # download and install emu
    git clone https://gitlab.com/treangenlab/emu.git
    mv emu /opt/	


    # install dependencies via conda
    conda install -c bioconda qcat yacrd nanofilt # qc softwares
    conda install -c bioconda -c conda-forge flatten-dict
    conda update --all