TomHarrop/singularity-containers:pinfish

$ singularity pull shub://TomHarrop/singularity-containers:pinfish

Singularity Recipe

Bootstrap: shub
From: TomHarrop/singularity-containers:racon_1.3.2

%help
    ONT Pinfish pipeline dependencies
    https://github.com/nanoporetech/pipeline-pinfish-analysis

%post
    # dependencies
    apt update
    apt install -y \
        cufflinks \
        git \
        python3 \
        python3-pip \
        samtools \
        zlib1g-dev

    # install conda
    wget -O install_miniconda.sh \
        --no-check-certificate \
        https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
    chmod 755 install_miniconda.sh
    ./install_miniconda.sh \
        -b \
        -p /miniconda
    export PATH="${PATH}:/miniconda/bin"
    rm -f install_miniconda.sh

    # install minimap2
    wget -O "minimap2.tar.gz" \
        --no-check-certificate \
        https://github.com/lh3/minimap2/archive/v2.11.tar.gz
    mkdir minimap2
    tar -zxf minimap2.tar.gz \
        -C minimap2 \
        --strip-components 1

    cd minimap2 || exit 1
    make
    mv minimap2 /usr/local/bin/

    cd .. || exit 1
    rm -rf minimap2 minimap2.tar.gz

    # install snakemake
    /usr/bin/pip3 install --upgrade pip
    /usr/local/bin/pip3 install snakemake

    # install pinfish
    git clone \
        --recursive \
        https://github.com/nanoporetech/pipeline-pinfish-analysis.git

%environment
    export PATH="${PATH}:/miniconda/bin"
    export PATH="${PATH}:/pipeline-pinfish-analysis/pinfish/cluster_gff"
    export PATH="${PATH}:/pipeline-pinfish-analysis/pinfish/collapse_partials"
    export PATH="${PATH}:/pipeline-pinfish-analysis/pinfish/polish_clusters"
    export PATH="${PATH}:/pipeline-pinfish-analysis/pinfish/spliced_bam2gff"

Collection

• Name: TomHarrop/singularity-containers
• License: None

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