hybpiper-paragone-singularity.def

BootStrap: library
From: ubuntu:22.04

%files

%post
    apt-get -y update
    apt-get install -y software-properties-common
    add-apt-repository universe
    apt-get -y update
    apt-get -y install curl
    apt-get -y install wget
    apt-get -y install git
    apt-get -y install time
    apt-get -y install locales
    apt-get -y install fonts-dejavu-core
    apt-get -y install build-essential
    apt-get -y install pkg-config
    apt-get -y install vim
    apt-get -y install unzip
    apt-get -y install libgl1 # necessary for ete3, see https://github.com/etetoolkit/ete/issues/195

    # install miniconda:
    if [ ! -d /usr/local/miniconda3 ]; then
        wget https://repo.anaconda.com/miniconda/Miniconda3-py39_24.4.0-0-Linux-x86_64.sh -O ~/miniconda.sh && \
        bash ~/miniconda.sh -b -p /usr/local/miniconda3 && \
        rm ~/miniconda.sh
    fi

    # set conda path:
    export PATH="/usr/local/miniconda3/bin:$PATH"

    # add bioconda and conda-forge channels:
    conda config --add channels defaults
    conda config --add channels bioconda
    conda config --add channels conda-forge


    # install programs using conda/mamba:
    conda install -c conda-forge mamba
    mamba install -y bioconda::paragone=1.1.3
    mamba install -y hybpiper=2.1.8
    mamba install -y bioconda::trimmomatic=0.39
    mamba install -y bioconda::fastp=0.23.2

%environment
    export PATH="/usr/local/miniconda3/bin:$PATH"
    export PATH="/fast-tree-install:$PATH"
    . /usr/local/miniconda3/etc/profile.d/conda.sh
    conda activate base

%runscript
    echo "This Singularity image is for use with the hybpiper.nf and paragone.nf scripts"

%labels
    Author Chris Jackson chris.jackson@rbgv.vic.gov.au