edg1983/Singularity_images:qcbam-v1.0.def

$ singularity pull shub://edg1983/Singularity_images:qcbam-v1.0.def

Singularity Recipe

Bootstrap: library
From: centos:8

%labels
    Author Edoardo Giacopuzzi
    Contact edoardo.giacopuzzi@well.ox.ac.uk

%help
    Image with alignment tools:
    - fastqc v0.11.9
    - samtools v1.11
    - mosdepth v0.3.1
    - somalier v0.2.12
    - multiqc v1.9

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

%post
    #yum update
    yum -y install \
        cmake \
        gcc \
        gcc-c++ \
        bzip2 \
        bzip2-devel \
        openssl-devel \
        xz-devel \
        openssl-devel \
        ncurses-devel \
        make \
        wget \
        zlib-devel \
        autoconf \
        tar \
        unzip \
        python3 \
        python3-devel \
        java-11-openjdk \
	procps

    yum -y groupinstall 'development tools'

    #install fastQC
    cd /opt
    wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zip
    unzip fastqc_v0.11.9.zip
    rm fastqc_v0.11.9.zip
    cd FastQC/
    chmod 755 fastqc
    cd /usr/local/bin 
    ln -s /opt/FastQC/fastqc ./
    
    #install samtools
    cd /opt
    wget https://github.com/samtools/samtools/releases/download/1.11/samtools-1.11.tar.bz2
    tar -jxvf samtools-1.11.tar.bz2
    rm samtools-1.11.tar.bz2
    cd samtools-1.11
    ./configure
    make
    make install

    #install mosdepth
    cd /usr/local/bin
    wget https://github.com/brentp/mosdepth/releases/download/v0.3.1/mosdepth
    chmod 755 mosdepth

    #install somalier 
    wget https://github.com/brentp/somalier/releases/download/v0.2.12/somalier
    chmod 755 somalier

    #install multiqc
    pip3 install multiqc

%test
    samtools --version
    somalier
    mosdepth -h
    multiqc --help
    fastqc --help

Collection


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key value
id /containers/edg1983-Singularity_images-qcbam-v1.0.def
collection name edg1983/Singularity_images
branch master
tag qcbam-v1.0.def
commit f4b53e73bdecc32b3168c64270ef1a86e9c2772a
version (container hash) 0e6774fb498512d7b961aeb3539a87e6428b0ee50758e6ae71f3ff1265e5b231
build date 2021-01-20T16:55:48.549Z
size (MB) 576.94921875
size (bytes) 604975104
SIF Download URL (please use pull with shub://)
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