TomHarrop/align-utils:salmontools_23eac84

$ singularity pull shub://TomHarrop/align-utils:salmontools_23eac84

Singularity Recipe

Bootstrap: library
From: ubuntu:20.04

%help

    Salmon 0.14.1
    https://github.com/COMBINE-lab/salmon/releases

%labels

    MAINTAINER "Tom Harrop (twharrop@gmail.com)"
    VERSION "salmon 0.14.1"

%post
    export DEBIAN_FRONTEND=noninteractive
    export LC_ALL=C

    # set up apt
    apt-get clean
    rm -r /var/lib/apt/lists/*
    apt-get  update
    apt-get upgrade -y --fix-missing
    (
        . /etc/os-release
        cat << _EOF_ > mirror.txt
deb mirror://mirrors.ubuntu.com/mirrors.txt ${UBUNTU_CODENAME} main restricted universe multiverse
deb mirror://mirrors.ubuntu.com/mirrors.txt ${UBUNTU_CODENAME}-updates main restricted universe multiverse
deb mirror://mirrors.ubuntu.com/mirrors.txt ${UBUNTU_CODENAME}-backports main restricted universe multiverse
deb mirror://mirrors.ubuntu.com/mirrors.txt ${UBUNTU_CODENAME}-security main restricted universe multiverse

_EOF_
        mv /etc/apt/sources.list /etc/apt/sources.list.bak
        cat mirror.txt /etc/apt/sources.list.bak > /etc/apt/sources.list
    )

    apt-get update
    apt-get install -y \
        build-essential \
        bedtools \
        cmake \
        curl \
        git \
        language-pack-en \
        wget \
        zlib1g-dev

    # install mashmap
    wget -O "mashmap.tar.gz" \
        --no-check-certificate \
        https://github.com/marbl/MashMap/releases/download/v2.0/mashmap-Linux64-v2.0.tar.gz
    mkdir mashmap
    tar -zxf mashmap.tar.gz \
        -C mashmap \
        --strip-components 1
    cp mashmap/mashmap /usr/local/bin/

    # build salmontools
    git clone https://github.com/COMBINE-lab/SalmonTools
    cd SalmonTools || exit 1
    git checkout 23eac84
    chmod -R 755 scripts
    mkdir build
    cd build || exit 1
    cmake ..
    make
    make install

%environment
    export PATH="${PATH}:/SalmonTools/scripts"

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

Collection


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Metrics

key value
id /containers/TomHarrop-align-utils-salmontools_23eac84
collection name TomHarrop/align-utils
branch master
tag salmontools_23eac84
commit 2b5b9827d1e469b5468ec0a10d67474a9817dea2
version (container hash) 485bd81250128259665ee3c198954204d3a4318d0499dd1090034c692b9aca9e
build date 2020-09-29T22:01:57.926Z
size (MB) 290.92578125
size (bytes) 305057792
SIF Download URL (please use pull with shub://)
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