Singularity

Bootstrap: docker
From: quay.io/biocontainers/braker2:2.1.6--hdfd78af_2

%environment
    export PATH=/opt/gmes_linux_64/ProtHint/bin/:${PATH}
    export AUGUSTUS_SCRIPTS_PATH=/usr/local/bin
    export AUGUSTUS_BIN_PATH=/usr/local/bin
    export GENEMARK_PATH=/opt/gmes_linux_64
    export ALIGNMENT_TOOL_PATH=/usr/local/bin/

# Register for GeneMark-ES/ET/EP at http://exon.gatech.edu/GeneMark/license_download.cgi (tested with ver 4.65)
# NOTE: the bundled license key expires after 200 days

%post
    set -o pipefail -o errexit
    readonly GENEMARK_DOWNLOAD_URL=http://topaz.gatech.edu/GeneMark/tmp/GMtool_v3gNp/gmes_linux_64.tar.gz
    wget -O - ${GENEMARK_DOWNLOAD_URL} | gzip -dc | tar -C /opt -xf -
    mkdir /opt/gm_key
    mv /opt/gmes_linux_64/gm_key /opt/gm_key/.gm_key
    cd /opt/gmes_linux_64
    perl change_path_in_perl_scripts.pl "/usr/bin/env perl"

    # https://github.com/gatech-genemark/ProtHint/issues/27
    sed -i.bak 's/grep -P/grep/' /opt/gmes_linux_64/ProtHint/bin/prothint.py
    sed -i.bak -e 's/readlink -e/realpath/' -e 's/stat --printf/stat -c/' /opt/gmes_linux_64/ProtHint/bin/spalnBatch.sh
   

%runscript
    exec braker.pl "$@"