knock-knock.def

Bootstrap: docker
From: debian:bookworm-slim

%labels
    Author knock-knock-local
    Version 0.8.2
    Description "knock-knock genome editing analysis tool (hits from PyPI)"
    Source https://github.com/jeffhussmann/knock-knock

%environment
    export PATH=/opt/conda/bin:$PATH
    export LC_ALL=C.UTF-8
    export LANG=C.UTF-8
    export MAMBA_ROOT_PREFIX=/opt/conda
    export MAMBA_NO_BANNER=1

%post
    set -e
    export PATH=/opt/conda/bin:/usr/local/bin:/usr/bin:/bin:$PATH
    export MAMBA_ROOT_PREFIX=/opt/conda
    export MAMBA_NO_BANNER=1
    apt-get update -qq && \
        apt-get install -y -q --no-install-recommends \
            wget ca-certificates bzip2 gcc libc6 libc6-dev libgcc-s1 bash git libc-bin libcrypt1 libtinfo6 ncurses-base && \
        rm -rf /var/lib/apt/lists/*

    # Install micromamba — standalone binary, no Anaconda/Miniconda license required
    mkdir -p /usr/local/bin
    wget -qO- "https://micro.mamba.pm/api/micromamba/linux-64/latest" \
        | tar -xj -C /usr/local/bin --strip-components=1 bin/micromamba
    micromamba shell init --shell bash --root-prefix /opt/conda

    micromamba install -y -p /opt/conda -c conda-forge -c bioconda \
        --channel-priority strict \
        python=3.12 \
        minimap2 \
        samtools \
        "blast>=2.7" \
        star \
        parallel \
        hdf5 > /dev/null

    # Upgrade pip
    pip install --upgrade pip

    pip install \
        "hits>=0.5.1" \
        anndata \
        "biopython>=1.86" \
        "bokeh>=2.4.2" \
        "h5py>=3.1.0" \
        "ipywidgets>=7.1.2" \
        "matplotlib>=2.1.2" \
        "nbconvert>=6.0.7" \
        "nbformat>=4.4.0" \
        "numpy>=1.14.2" \
        "pandas>=0.22.0" \
        "Pillow>=5.0.0" \
        "pysam>=0.14" \
        "PyYAML>=3.12" \
        "scipy>=1.16.2" \
        tables \
        "tqdm>=4.31.1" \
        "viennarna>=2.6.4"

    # Install knock-knock from the upstream GitHub repo
    pip install git+https://github.com/jeffhussmann/knock-knock.git

    # Clean up to reduce image size
    micromamba clean -a -y
    pip cache purge

%test
	echo "=== knock-knock container smoke tests ==="
	knock-knock --help > /dev/null         && echo "PASS: knock-knock CLI"
	python -c "
import knock_knock, hits
print(f'PASS: knock_knock {knock_knock.__version__}')
print(f'PASS: hits {hits.__version__}')
"
	minimap2 --version                     && echo "PASS: minimap2"
	samtools --version 2>&1 | head -1      && echo "PASS: samtools"
	blastn -version    2>&1 | head -1      && echo "PASS: blastn"
	STAR --version     2>&1 | head -1      && echo "PASS: STAR"
	parallel --version 2>&1 | head -1      && echo "PASS: GNU parallel"

%help
    knock-knock: genome editing outcome analysis tool
    https://github.com/jeffhussmann/knock-knock

    This container installs the 'hits' dependency from PyPI rather than bioconda,
    working around a known issue with the bioconda-packaged hits version.

    Basic usage:
        apptainer exec knock-knock.sif knock-knock --help
        apptainer exec -B /path/to/data:/data knock-knock.sif \
			knock-knock process-sample <args>