Bootstrap: localimage
From: sif/build/ubuntu-22.04.sif

%post
    apt-get update
    apt-get install -qq curl bzip2 gcc make zlib1g-dev libbz2-dev liblzma-dev libdeflate-dev git python3-pip python3

    apt install ncbi-blast+  --assume-yes

    mkdir -p /opt/trf/
    curl -Ls -o /opt/trf/trf "https://github.com/Benson-Genomics-Lab/TRF/releases/download/v4.09.1/trf409.linux64"
    chmod +x /opt/trf/trf

    # bedtools
    curl -Ls -o /usr/local/bin/bedtools https://github.com/arq5x/bedtools2/releases/download/v2.30.0/bedtools.static.binary
    echo "e85d74b6c11b664c05176b1dbf7d2891ad0383ae93805db2d29034db5c2d80ce  /usr/local/bin/bedtools" | sha256sum -c
    chmod +x /usr/local/bin/bedtools

    pip install git+https://github.com/bcgsc/straglr.git@v1.5.3#egg=straglr

    # cleanup
    pip cache purge
    apt-get clean

%environment
   PATH=$PATH:/opt/trf:/usr/local/bin/bedtools

%help
    Long-read-based human genomic short tandem repeat detection.
