pst-classifier.def

Bootstrap: docker
From: debian:bullseye

%files
    include /PstClassifierSeqan/include
    src /PstClassifierSeqan/src
    tests /PstClassifierSeqan/tests
    seqan3 /PstClassifierSeqan/seqan3
    eigen /PstClassifierSeqan/eigen
    HighFive /PstClassifierSeqan/HighFive
    robin-hood-hashing /PstClassifierSeqan/robin-hood-hashing
    indicators /PstClassifierSeqan/indicators
    vlmc-from-kmers /PstClassifierSeqan/vlmc-from-kmers
    CMakeLists.txt /PstClassifierSeqan/CMakeLists.txt
    ../kmc /kmc

%post
    apt-get update -y && apt-get install -y cmake build-essential g++ git gcc

    apt-get install -y libhdf5-dev libeigen3-dev libtbb-dev libgomp1 doxygen libboost-all-dev

    mkdir /PstClassifierSeqan/build
    cd /PstClassifierSeqan/build

    cmake -DCMAKE_BUILD_TYPE=Release ..
    make bic pst-batch-training pst-classifier pst-score-sequences calculate-distances

    cp /kmc/KMC3.linux/kmc /kmc/KMC3.linux/kmc_tools /PstClassifierSeqan/build/src/

%environment
    export PATH="/PstClassifierSeqan/build/src/:$PATH"

%test
    #cd /PstClassifierSeqan/build/tests
    echo "Running tests"
    bic -h
    pst-classifier -h
    pst-score-sequences -h
    calculate-distances

%apprun bic
    cd /PstClassifierSeqan/build/src/
    /PstClassifierSeqan/build/src/bic $*

%apprun score
    cd /PstClassifierSeqan/build/src/
    /PstClassifierSeqan/build/src/pst-score-sequences $*

%apprun build
    cd /PstClassifierSeqan/build/src/
    /PstClassifierSeqan/build/src/pst-classifier $*

%apprun distances
    cd /PstClassifierSeqan/build/src/
    /PstClassifierSeqan/build/src/calculate-distances $*