cistopic_singularity.def

Bootstrap: scratch

%setup
    alpine_lastest_stable_base_url='http://dl-cdn.alpinelinux.org/alpine/latest-stable/releases/x86_64'

    # Get url of last stable version of alpine minirootfs:
    #   - Parse YAML file with info about lastest releases.
    #   - Get url of the first "Mini root filesystem" section.
    alpine_minirootfs_url=$(
        curl "${alpine_lastest_stable_base_url}/latest-releases.yaml" \
          | awk \
                -F ': ' \
                -v "alpine_lastest_stable_base_url=${alpine_lastest_stable_base_url}" '
                {
                    if ( $1 ~ "  title" ) {
                        if ($2 == "\"Mini root filesystem\"" ) {
                            mini_root_filesystem_section = 1;
                        } else {
                            mini_root_filesystem_section = 0;
                        }
                    } else if ( mini_root_filesystem_section == 1 && $1 == "  file") {
                        # Print full url to Alpine minirootfs.
                        printf("%s/%s", alpine_lastest_stable_base_url, $2);
                        mini_root_filesystem_file_found = 1;
                        exit 0;
                    }
                }
                END {
                    if ( mini_root_filesystem_file_found != 1 ) {
                        # Unable to find minirootfs url.
                        printf("%s", "error");
                    }
                }
                '
    )

    if [ "${alpine_minirootfs_url}" = "error" ] ; then
        printf 'Error: Unable to find last stable version of alpine minirootfs url.';
        exit 1;
    fi

    # Download and extract alpine minirootfs.
    curl ${alpine_minirootfs_url} \
       | tar xz -C "${SINGULARITY_ROOTFS}" --exclude=./dev --exclude=./etc/hosts

%post
    export LANG=en_US.UTF-8

    # Use a custom TMP dir for manually downloadeded packages.
    export TMPDIR=$(mktemp -t -d cistopic_singularity_XXXXXX);

    # Update package list.
    apk update

    # Upgrade installed packages.
    apk upgrade

    # Install needed packages to download, compile and run R packages.
    apk add \
        build-base expat expat-dev libxml2 libxml2-dev \
        autoconf automake libtool curl R R-dev R-doc git


    # Function to install a CRAN package.
    install_CRAN_package () {
        local CRAN_package="${1}"

        printf 'if (!require("%s", character.only=TRUE, quietly=TRUE)) {\n    install.packages(c("%s"), repo=c(CRAN = "https://cloud.r-project.org"));\n}\nq();\n' \
            "${CRAN_package}" \
            "${CRAN_package}" \
          | R --vanilla --quiet
    }

    # Function to Install a Bioconductor packages.
    install_Bioconductor_package () {
        local bioconductor_package="${1}"

        printf 'if (!require("%s", character.only=TRUE, quietly=TRUE)) {\n    require(BiocManager);\n    BiocManager::install(c("%s"));\n}\nq();\n' \
            "${bioconductor_package}" \
            "${bioconductor_package}" \
          | R --vanilla --quiet
    }


    ## Install httpuv manually as installing it directly from R does not work.

    httpuv_version='1.4.5.1'

    httpuv_CRAN_packages='
        Rcpp
        promises
        later
        BH
    '

    # Install list of CRAN packages needed to install httpuv.
    for CRAN_package in ${httpuv_CRAN_packages} ; do
        printf '\nInstalling CRAN package: "%s"\n\n' "${CRAN_package}"
        install_CRAN_package "${CRAN_package}"
    done

    # Download httpuv tarball.
    curl \
        -o "${TMPDIR}/httpuv_${httpuv_version}.tar.gz" \
        "https://cloud.r-project.org/src/contrib/httpuv_${httpuv_version}.tar.gz"

    # Extract httpuv tarball.
    tar xz -C ${TMPDIR} -f "${TMPDIR}/httpuv_${httpuv_version}.tar.gz"

    # Regenerate automake config files for libuv.
    cd ${TMPDIR}/httpuv/src/libuv/ && aclocal && autoconf && automake && cd -

    # Install httpuv.
    R CMD INSTALL ${TMPDIR}/httpuv

    # Remove downloaded and extracted httpuv related files.
    rm -r ${TMPDIR}/httpuv "${TMPDIR}/httpuv_${httpuv_version}.tar.gz"


    ## Install udunits2 manually as it is not in the apk package manager.

    udunits2_version='2.2.26'

    # Download udunits2 tarball.
    curl \
        -o "${TMPDIR}/udunits-${udunits2_version}.tar.gz" \
        "ftp://ftp.unidata.ucar.edu/pub/udunits/udunits-${udunits2_version}.tar.gz"

    # Extract udunits2 tarball.
    tar xz -C ${TMPDIR} -f "${TMPDIR}/udunits-${udunits2_version}.tar.gz"

    # Configure and install udunits2.
    cd ${TMPDIR}/udunits-${udunits2_version} && ./configure && make && make install && cd -

    # Remove downloaded and extracted udunits2 related files.
    rm -r "${TMPDIR}/udunits-${udunits2_version}" "${TMPDIR}/udunits-${udunits2_version}.tar.gz"


    ## Install R dependencies for cisTopic.

    # List of CRAN packages.
    CRAN_packages='
        BiocManager
        data.table
        doSNOW
        DT
        fastcluster
        feather
        fitdistrplus
        ggplot2
        knitr
        lda
        Matrix
        plotly
        plyr
        rmarkdown
        Rtsne
        R.utils
        scatterplot3d
        tibble
        umap
    '

    # List of Bioconductor packages.
    bioconductor_packages='
        BiocGenerics
        BiocStyle
        GenomicRanges
        ChIPseeker
        ComplexHeatmap
        destiny
        GSEABase
        Rsubread
        rGREAT
        rtracklayer
        S4Vectors
        SummarizedExperiment
        AUCell
        RcisTarget
    '

    # Install list of CRAN packages.
    for CRAN_package in ${CRAN_packages} ; do
        printf '\nInstalling CRAN package: "%s"\n\n' "${CRAN_package}"
        install_CRAN_package "${CRAN_package}"
    done

    # Install list of BioConductor packages.
    for bioconductor_package in ${bioconductor_packages} ; do
        printf '\nInstalling Bioconductor package: "%s"\n\n' "${bioconductor_package}"
        install_Bioconductor_package "${bioconductor_package}"
    done


    ## cisTopic installation.

    # Clone cisTopic git repository.
    git clone --depth 1 https://github.com/aertslab/cisTopic ${TMPDIR}/cisTopic-git

    # Install cisTopic.
    R CMD INSTALL ${TMPDIR}/cisTopic-git

    # Remove cisTopic git repository.
    rm -rf ${TMPDIR}/cisTopic-git


    # Remove build dependencies.
    apk del build-base expat-dev libxml2-dev autoconf automake libtool R-dev R-doc git

%runscript
    R "${@}"

%labels
    Maintainer Gert Hulselmans
    Package cisTopic
    Version v0.2.0
    URL https://github.com/aertslab/cisTopic

%environment
    export R_MAX_NUM_DLLS=500

%help
    For help see: https://rawcdn.githack.com/aertslab/cisTopic/f6091ff94c79dfc927ae8eddf201d10a3f092923/vignettes/CompleteAnalysis.html