edg1983/Singularity_images:hapcut2.def

$ singularity pull shub://edg1983/Singularity_images:hapcut2.def

Singularity Recipe

Bootstrap: docker
From: ubuntu:bionic

%environment
    SHELL=/bin/bash
    PATH=$PATH:/usr/local/bin
    export C_INCLUDE_PATH=$C_INCLUDE_PATH:/opt/htslib-1.11
    export LIBRARY_PATH=$LIBRARY_PATH:/opt/htslib-1.11
    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/htslib-1.11
    LC_ALL=C.UTF-8


%help
    HapCUT2 container latest version from
    https://github.com/vibansal/HapCUT2

    Available commands: HAPCUT2, extractHAIRS

%post
    apt-get update
    apt-get -y install apt-transport-https \
        build-essential \
        cmake \
        gcc \
        language-pack-en-base \
        libbz2-dev \
        libcurl4-openssl-dev \
        liblzma-dev \
        libncurses5-dev \
        libreadline-dev \
        libssl-dev \
        git \
        make \
        wget \
        zlib1g-dev \
        autoconf
    update-locale LC_ALL=en_US.UTF-8 LANG=en_US.UTF-8
    
    ## Install HTSlib
    cd /opt
    wget https://github.com/samtools/htslib/releases/download/1.11/htslib-1.11.tar.bz2
    tar -jxvf htslib-1.11.tar.bz2
    rm htslib-1.11.tar.bz2
    cd htslib-1.11
    make
    make install

    ## Install HapCUT2
    cd /opt
    git clone https://github.com/vibansal/HapCUT2.git
    cd HapCUT2
    make HTSLIB=/opt/htslib-1.11
    ln -s /opt/HapCUT2/build/HAPCUT2 /usr/local/bin/HAPCUT2
    ln -s /opt/HapCUT2/build/extractHAIRS /usr/local/bin/extractHAIRS

Collection


View on Datalad

Metrics

key value
id /containers/edg1983-Singularity_images-hapcut2.def
collection name edg1983/Singularity_images
branch master
tag hapcut2.def
commit 85f26be1c0a2aaec4d4eba251bcf1f24da53987f
version (container hash) c4fbd7f59a48376b88c031973e37769dafcb9dd0cb109881741497d4c19f7fdd
build date 2020-11-02T10:32:54.635Z
size (MB) 196.96875
size (bytes) 206536704
SIF Download URL (please use pull with shub://)
Datalad URL View on Datalad
Singularity Recipe Singularity Recipe on Datalad
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