Virsorter

Virsorter 2 can be built with the database in the image. In the tempalate I commented out those steps assuming the Database will be stored elsewhere.

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 create -p /opt/software/conda_env -y {package}={version}
    source /opt/software/conda/bin/activate /opt/software/conda_env
    #virsorter setup -d /opt/software/conda_env/virsorter-db -j 2
    #ls -l /opt/software/conda_env/virsorter-db/
    #find /opt/software/conda_env/virsorter-db/ -type d -exec chmod a+rx '{}' \;
    #find /opt/software/conda_env/virsorter-db/ -type f -exec chmod a+r  '{}' \;
    cd /opt/software

%runscript
    exec {binary} "$@"

  

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