Sigularity def for Pangolin https://github.com/cov-lineages/pangolin

pangolin.def

Bootstrap: docker
From: ubuntu:xenial


%labels
    Author: Thanh Le Viet
    Software: pangolin
    Description: "Pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages"
    Notes: "This singularity definition is based on https://github.com/StaPH-B/docker-builds"

# ENV PANGOLIN_VERSION "2.0.1"
# ENV PANGOLIN_LEARN_VERSION "2020-07-20"

# LABEL base.image="ubuntu:xenial"
# LABEL dockerfile.version="1"
# LABEL software="pangolin"
# LABEL software.version=${PANGOLIN_VERSION}
# LABEL description="Conda environment for Pangolin. Pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages."
# LABEL website="https://github.com/hCoV-2019/pangolin"
# LABEL license="GNU General Public License v3.0"
# LABEL license.url="https://github.com/hCoV-2019/pangolin/blob/master/LICENSE.txt"
# LABEL maintainer="Erin Young"
# LABEL maintainer.email="[email protected]"

%setup
    # set the environment

%files

%environment
    export PATH="/miniconda/envs/pangolin/bin:$PATH"
    export LC_ALL=C

%post
    PANGOLIN_VERSION="2.1.2"
    PANGOLIN_LEARN_VERSION="2020-07-20"
    export LC_ALL=C
    export ROOT_CONDA="/miniconda"
    export PATH="${ROOT_CONDA}/bin:$PATH"
    # install needed software for conda install
    apt-get update && apt-get install -y \
    wget \
    git \
    build-essential \
    && rm -rf /var/lib/apt/lists/*

    cd /opt
    # get miniconda and the pangolin repo
    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh &&\
    bash ./Miniconda3-latest-Linux-x86_64.sh -p /miniconda -b  &&\
    rm Miniconda3-latest-Linux-x86_64.sh &&\
    conda install -c conda-forge mamba

    wget https://github.com/cov-lineages/pangolin/archive/v${PANGOLIN_VERSION}.tar.gz &&\
    tar -xf v${PANGOLIN_VERSION}.tar.gz &&\
    mv pangolin-${PANGOLIN_VERSION} pangolin


    # create the conda environment and set as default
    conda env create -f pangolin/environment.yml
    echo "source activate pangolin" > /etc/bash.bashrc

    conda clean --all -y
    export PYTHON="/miniconda/envs/pangolin/bin/python"
    export PATH="/miniconda/envs/pangolin/bin:$PATH"
    cd pangolin && \
    $PYTHON setup.py install
    # install and update pangolin learn
    # do it here to allow for caching of the previous layers

    #Just install latest update
    $PYTHON -m pip install git+https://github.com/cov-lineages/pangoLEARN.git

    $PYTHON -m pip install git+https://github.com/cov-lineages/lineages.git

%test
    export PATH="/miniconda/envs/pangolin/bin:$PATH"
    pangolin -v && pangolin -lv && pangolin -pv