TomHarrop/pollen-its-wrapper:v0.0.3

$ singularity pull shub://TomHarrop/pollen-its-wrapper:v0.0.3

Singularity Recipe

Bootstrap: docker
From: rocker/verse:4.0.3

%help
    Container for pollen-its-wrapper v0.0.3

%labels
    VERSION "pollen-its-wrapper v0.0.3"
    MAINTAINER "Tom Harrop"

%post
    export DEBIAN_FRONTEND=noninteractive
    export LC_ALL=C

    # install dependencies
    apt-get update
    apt-get install -y \
        libbz2-dev \
        liblzma-dev \
        libpcre++-dev \
        python3-pip

    # install packages from bioconductor
    Rscript -e "options(Ncpus=8); \
        install.packages('BiocManager') ; \
        BiocManager::install(c(\
            'dada2', \
            'data.table', \
            'gtools'), 
            type='source', ask=FALSE)"

    /usr/bin/python3 -m pip \
        install --upgrade \
        pip \
        setuptools \
        wheel

    /usr/bin/python3 -m pip \
        install \
    	biopython==1.78 \
        cutadapt==3.1 \
        pandas==1.1.5 \
        snakemake==5.31.1

    # install pipeline
    /usr/bin/python3 -m pip \
        install \
        git+git://github.com/tomharrop/pollen-its-wrapper.git@v0.0.3

%runscript
    exec /usr/local/bin/pollen_its_wrapper "$@"

Collection


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Metrics

key value
id /containers/TomHarrop-pollen-its-wrapper-v0.0.3
collection name TomHarrop/pollen-its-wrapper
branch master
tag v0.0.3
commit 69cf3b435b0524b7437af495abcb9407852d4c4b
version (container hash) ae57dab3ff0bbb8869ffa24bf39531b507d472fc790ab5e90117b5b67ad8a298
build date 2020-12-22T02:47:35.030Z
size (MB) 1463.02734375
size (bytes) 1534095360
SIF Download URL (please use pull with shub://)
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