edg1983/Singularity_images:vcf_processing.def

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

Singularity Recipe

Bootstrap: library
From: centos:8

%environment
    SHELL=/bin/bash
    PATH=$PATH:/usr/local/bin
    LC_ALL=C.UTF-8

%help
    Set of tools to process and QC a VCF file.
    Includes: bcftools, vt, multiqc and a custom script (VCF_fixes_opt)

%post
    yum -y install cmake \
        curl \
        gcc \
        gcc-c++ \
        git \
        bzip2 \
        bzip2-devel \
        openssl-devel \
        xz-devel \
        openssl-devel \
        ncurses-devel \
        make \
        wget \
        zlib-devel \
        autoconf \
        tar \
        unzip \
        python3 \
        python3-devel \
        procps
    
    ## Install bcftools and htslib
    cd /opt/ && wget https://github.com/samtools/bcftools/releases/download/1.10.2/bcftools-1.10.2.tar.bz2
    tar -jxvf bcftools-1.10.2.tar.bz2
    rm bcftools-1.10.2.tar.bz2
    cd bcftools-1.10.2
    ./configure
    make
    make install
    cd htslib-1.10.2
    ./configure
    make
    make install

    #install vt
    cd /opt
    wget https://github.com/atks/vt/archive/0.5772.tar.gz  
    tar -zxvf 0.5772.tar.gz
    rm 0.5772.tar.gz
    cd vt-0.5772
    make

    #install multiqc
    pip3 install multiqc

    #Get compiled VCF_fixes_opt
    cd /opt
    wget https://github.com/edg1983/VCF_fixes/raw/master/VCF_fixes
    chmod a+x VCF_fixes

    #Make links
    cd /usr/local/bin
    ln -s /opt/vt-0.5772/vt vt
    ln -s /opt/VCF_fixes VCF_fixes

%test
    bcftools --help
    vt
    multiqc --help
    VCF_fixes --help

Collection


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Metrics

key value
id /containers/edg1983-Singularity_images-vcf_processing.def
collection name edg1983/Singularity_images
branch master
tag vcf_processing.def
commit 3a1dcaecf83a5bb3fc3c4ce573dccd2be3c13ade
version (container hash) 19e60a30382e9861cbfd11337960829f17a828b592c8ee38b520056cc4a404c8
build date 2021-01-20T17:10:10.597Z
size (MB) 366.5
size (bytes) 384303104
SIF Download URL (please use pull with shub://)
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