scramble.def

Bootstrap: docker
From: ubuntu:20.04

%post
    export TZ='Europe/Amsterdam'
    export DEBIAN_FRONTEND=noninteractive
    
    apt-get clean all && \
    apt-get update && \
    apt-get upgrade -y && \
    apt-get install -y  \
        autoconf \
        autogen \
        build-essential \
        curl \
        libbz2-dev \
        libcurl4-openssl-dev \
        libhts3 \
        libhts-dev \
        liblzma-dev \
        libncurses5-dev \
        libnss-sss \
        libssl-dev \
        libxml2-dev \
        ncbi-blast+ \
        zlib1g-dev \
        git

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

    # Installing R 4.3
    sed -i.bak "/^#.*deb-src.*universe$/s/^# //g" /etc/apt/sources.list
    apt -y update
    apt -y build-dep r-base
    export R_VERSION=4.3.1
    curl -O https://cran.rstudio.com/src/base/R-4/R-${R_VERSION}.tar.gz
    tar -xzvf R-${R_VERSION}.tar.gz
    cd R-${R_VERSION}
    ./configure \
        --prefix=/opt/R/${R_VERSION} \
        --enable-R-shlib \
        --enable-memory-profiling \
        --with-blas\
        --with-lapack
    make
    make install
    ln -s /opt/R/${R_VERSION}/bin/R /usr/local/bin/R
    ln -s /opt/R/${R_VERSION}/bin/Rscript /usr/local/bin/Rscript
    cd ..

    # Set CRAN mirror in Rprofile
    echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.us.r-project.org'; options(repos = r);" > /root/.Rprofile

    # Install BiocManager
    R --slave -e 'if(!require("BiocManager", quietly=TRUE)) install.packages("BiocManager")'
    R --slave -e 'install.packages(c("optparse", "stringr", "devtools"))'
    R --slave -e 'devtools::install_github("mhahsler/rBLAST")'


    # Install rBLAST from BCmanager
    R --slave -e 'BiocManager::install(c("Biostrings", "Rsamtools"))'
    
    # install scramble
    cd app
    git clone https://github.com/GeneDx/scramble.git
    cd scramble
    cd cluster_identifier/src
    make
    ln -s /app/scramble/cluster_identifier/src/build/cluster_identifier /usr/local/bin/cluster_identifier

%environment
    export PATH=/usr/local/bin:$PATH

%files
    . /app
    . /mnt/source

%labels
    Author Tim Niemeijer