TomHarrop/singularity-containers:basecall_wrapper_0.0.30_albacore_2.3.3

$ singularity pull shub://TomHarrop/singularity-containers:basecall_wrapper_0.0.30_albacore_2.3.3

Singularity Recipe

Bootstrap: docker
From: rocker/tidyverse:3.5.1

%help

    basecall_wrapper 0.0.30 with Python 3.5.3 and albacore 2.3.3
    
%labels

    MAINTAINER "Tom Harrop (twharrop@gmail.com) "
    VERSION "basecall_wrapper 0.0.30 with albacore 2.3.3"

%runscript

    exec /usr/local/bin/basecall_wrapper "$@"

%post

    # install apt packages
    apt-get update
    apt-get install -y \
        default-jre \
        python3-pip

    # install bbmap
    wget -O "bbmap.tar.gz" \
        "https://sourceforge.net/projects/bbmap/files/BBMap_38.00.tar.gz"
    mkdir bbmap-install
    tar -zxf bbmap.tar.gz \
        -C bbmap-install \
        --strip-components 1
    cp -r bbmap-install/resources/* /
    cp -r bbmap-install/* /usr/local/bin/
    rm -rf bbmap.tar.gz bbmap-install

    # install python bits
    pip3 install --upgrade pip
    /usr/local/bin/pip3 install \
        biopython \
        numpy \
        pathlib2 \
        psutil \
        snakemake

    # install albacore
    /usr/local/bin/pip3 install \
        https://mirror.oxfordnanoportal.com/software/analysis/ont_albacore-2.3.3-cp35-cp35m-manylinux1_x86_64.whl

    # install basecall_wrapper
    /usr/local/bin/pip3 install git+git://github.com/tomharrop/basecall_wrapper.git

    # lanfear QC script
    Rscript -e "install.packages(c( \
        'futile.logger', \
        'optparse', \
        'viridis'))"

    wget \
        -O /usr/local/bin/MinIONQC.R \
        https://raw.githubusercontent.com/roblanf/minion_qc/master/MinIONQC.R
    chmod 755 /usr/local/bin/MinIONQC.R

    # link R
    ln -s /usr/local/bin/Rscript /usr/bin/Rscript

Collection

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

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