remiolsen/qaTools-singularity:latest

$ singularity pull shub://remiolsen/qaTools-singularity:latest

Singularity Recipe

BootStrap: docker
From: debian:9

%label
    Maintainer remi-andre.olsen@scilifelab.se

%post
    apt-get update
    apt-get install -y git build-essential autoconf zlib1g-dev libbz2-dev liblzma-dev wget

    #Fetch things
    wget https://downloads.sourceforge.net/project/samtools/samtools/1.3/samtools-1.3.tar.bz2
    wget https://downloads.sourceforge.net/project/samtools/samtools/1.3/htslib-1.3.tar.bz2
    tar xfj samtools-1.3.tar.bz2
    tar xfj htslib-1.3.tar.bz2
    rm *.bz2
    git clone https://github.com/vezzi/qaTools.git

    #samtools
    cd samtools-1.3
    autoconf -Wno-syntax
    ./configure --without-curses
    make
    make install
    cd htslib-1.3 
    make
    make install
    cd ../..
    cp /usr/local/lib/libhts.* /lib

    #qaTools
    cd qaTools
    make SAMTOOLS=../samtools-1.3 VERSION=1.3
    cp computeInsertSizeHistogram /bin
    cp doBWAQualTrimming /bin
    cp qaCompute /bin
    cp removeUnmapped /bin

    #UPPMAX stuff NOTE: Only testing for now, should use singulary run -B /sw:/sw etc container.img
    mkdir /sw
    mkdir /proj
    mkdir /pica
    mkdir /lupus

    apt-get clean
    rm -rf /var/lib/apt/lists/*

%runscript
    exec qaCompute "$@"

Collection

• Name: remiolsen/qaTools-singularity
• License: None

Metrics

Feedback

Was this page helpful?

Glad to hear it! Please tell us how we can improve.

Sorry to hear that. Please tell us how we can improve.