Using_mamba

This is an example of using mamba instead of conda for faster image generation.

To be used with the fill_template tool.

Bootstrap: docker
From: centos:centos7.6.1810


%environment
    export PATH=$PATH:/opt/software/conda/bin/
    source /opt/software/conda/bin/activate /opt/software/conda_env


%post
    yum -y install epel-release wget which nano curl zlib-devel
    yum -y groupinstall "Development Tools"

    mkdir -p /opt/software

    cd /opt/software
    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 defaults
    /opt/software/conda/bin/conda config --add channels conda-forge
    /opt/software/conda/bin/conda config --add channels bioconda
    /opt/software/conda/bin/conda install -y -c conda-forge mamba
    /opt/software/conda/bin/mamba create -p /opt/software/conda_env -y "python>=3.6" scikit-learn=0.22.1 imbalanced-learn pandas seaborn hmmer prodigal screed ruamel.yaml "snakemake>=5.16,<=5.26" click virsorter=2.0
    source /opt/software/conda/bin/activate /opt/software/conda_env
    cd /opt/software

%runscript
    exec virsorter "$@"

  

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