bioinformatics-group/bioinformatics-singularity:latest

$ singularity pull shub://bioinformatics-group/bioinformatics-singularity:latest

Singularity Recipe

Bootstrap: debootstrap
OSVersion: stretch
MirrorURL: http://ftp.ca.debian.org/debian/

%files
    setup.R

%post
    export DEBIAN_FRONTEND=noninteractive
    apt-get update
    apt-get install -y curl gnupg2
    apt-get install -y ca-certificates lsb-release apt-transport-https dirmngr
    curl --silent -o apt.gpg https://packages.sury.org/php/apt.gpg
    echo "deb http://cran.rstudio.com/bin/linux/debian stretch-cran35/" >> /etc/apt/sources.list
    apt-key add /apt.gpg
    apt-key adv --keyserver keys.gnupg.net --recv-key 'E19F5F87128899B192B1A2C2AD5F960A256A04AF'
    apt-get -qqq update
    apt-get -qqq upgrade
    ln -fs /usr/share/zoneinfo/America/New_York /etc/localtime
    dpkg-reconfigure --frontend noninteractive tzdata
    apt-get -y install gfortran g++ perl alien git r-base libcurl4-openssl-dev libxml2-dev
    Rscript setup.R
    curl -s ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.3.0/ncbi-blast-2.3.0+-1.x86_64.rpm --output ncbi-blast-2.3.0+-1.x86_64.rpm
    alien -i ncbi-blast-2.3.0+-1.x86_64.rpm
    git clone https://github.com/cbcrg/tcoffee.git tcoffee
    cd tcoffee/compile
    make t_coffee
    cp t_coffee /usr/bin/
    cd ../..
    rm -r tcoffee
    apt-get update && apt-get install -y && \
           apt-get install -y locales locales-all && \
            export LANGUAGE=en_US.UTF-8 && \
            export LANG=en_US.UTF-8 && \
            export LC_ALL=en_US.UTF-8 && \
            locale-gen en_US.UTF-8 && \
            dpkg-reconfigure locales
    rm ncbi-blast-2.3.0+-1.x86_64.rpm
    rm -r /var/lib/apt/lists/*

Collection

• Name: bioinformatics-group/bioinformatics-singularity
• License: MIT License

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