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adding clair3 version 1.0.10 (#1035)
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| ARG CLAIR3_VER="1.0.10" | ||
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| FROM mambaorg/micromamba:1.5.8 as builder | ||
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| ARG CLAIR3_VER | ||
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| USER root | ||
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| WORKDIR / | ||
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| RUN apt-get update && apt-get install -y \ | ||
| wget \ | ||
| bzip2 \ | ||
| make \ | ||
| g++ \ | ||
| libboost-graph-dev | ||
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| RUN micromamba install --name base -c conda-forge -c bioconda \ | ||
| python=3.9.0 \ | ||
| pypy3.6 \ | ||
| tensorflow-cpu=2.8.0 \ | ||
| pytables \ | ||
| pigz \ | ||
| cffi=1.14.4 \ | ||
| parallel=20191122 \ | ||
| zstd \ | ||
| samtools=1.15.1 \ | ||
| whatshap=1.7 \ | ||
| xz \ | ||
| zlib \ | ||
| bzip2 \ | ||
| automake \ | ||
| curl &&\ | ||
| micromamba clean -a -y | ||
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| ENV PATH="$PATH:/opt/conda/bin/" | ||
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| ARG MAMBA_DOCKERFILE_ACTIVATE=1 | ||
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| RUN pypy3 -m ensurepip && \ | ||
| pypy3 -m pip install mpmath==1.2.1 &&\ | ||
| pip install tensorflow-addons | ||
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| RUN wget -q https://github.com/HKU-BAL/Clair3/archive/refs/tags/v${CLAIR3_VER}.tar.gz &&\ | ||
| tar -xvf v${CLAIR3_VER}.tar.gz &&\ | ||
| cd Clair3-${CLAIR3_VER}/preprocess/realign/ &&\ | ||
| g++ -std=c++14 -O1 -shared -fPIC -o realigner ssw_cpp.cpp ssw.c realigner.cpp && \ | ||
| g++ -std=c++11 -shared -fPIC -o debruijn_graph -O3 debruijn_graph.cpp &&\ | ||
| cd ../.. &&\ | ||
| make &&\ | ||
| mkdir /clair3 &&\ | ||
| cp -rv clair3 preprocess postprocess scripts shared /clair3 &&\ | ||
| cp clair3.py run_clair3.sh /clair3 &&\ | ||
| cp longphase libclair3* /clair3 &&\ | ||
| cp LICENSE.md /clair3 | ||
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| RUN mkdir /clair3/models &&\ | ||
| wget -q http://www.bio8.cs.hku.hk/clair3/clair3_models/clair3_models.tar.gz &&\ | ||
| tar --no-same-owner -C /clair3/models -xvf clair3_models.tar.gz | ||
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| ## App ## | ||
| FROM mambaorg/micromamba:1.5.8 as app | ||
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| ARG CLAIR3_VER | ||
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| USER root | ||
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| WORKDIR / | ||
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| LABEL base.image="mambaorg/micromamba:1.5.8" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="CLAIR3" | ||
| LABEL software.version="${CLAIR3_VER}" | ||
| LABEL description="Clair3 is a germline small variant caller for long-reads." | ||
| LABEL website="https://github.com/HKU-BAL/Clair3" | ||
| LABEL license="https://github.com/HKU-BAL/Clair3/blob/main/LICENSE.md" | ||
| LABEL maintainer="Kutluhan Incekara" | ||
| LABEL maintainer.email="[email protected]" | ||
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| RUN apt-get update && apt-get install --no-install-recommends -y\ | ||
| procps && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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| RUN micromamba install --name base -c conda-forge -c bioconda \ | ||
| python=3.9.0 \ | ||
| numpy=1.24.3 \ | ||
| pypy3.6 \ | ||
| tensorflow-cpu=2.8.0 \ | ||
| pytables \ | ||
| pigz \ | ||
| cffi=1.14.4 \ | ||
| parallel=20191122 \ | ||
| zstd \ | ||
| samtools=1.15.1 \ | ||
| whatshap=1.7 &&\ | ||
| micromamba clean -a -y &&\ | ||
| rm -rf /opt/conda/pkgs/ | ||
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| ENV PATH="/opt/conda/bin/:/clair3:${PATH}" \ | ||
| LC_ALL=C.UTF-8 | ||
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| RUN pypy3 -m ensurepip &&\ | ||
| pypy3 -m pip install --no-cache mpmath==1.2.1 &&\ | ||
| pip install --no-cache tensorflow-addons | ||
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| COPY --from=builder /clair3 /clair3 | ||
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| CMD run_clair3.sh | ||
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| WORKDIR /data | ||
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| ## Test ## | ||
| FROM app as test | ||
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| RUN run_clair3.sh | ||
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| RUN apt-get update && apt-get install -y wget | ||
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| RUN wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/clair3/1.0.9/ont_quick_test.sh && \ | ||
| chmod +x ont_quick_test.sh &&\ | ||
| ./ont_quick_test.sh |
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| # Clair3 container | ||
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| Main tool: [clair3](https://github.com/HKU-BAL/Clair3) | ||
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| Code repository: https://github.com/HKU-BAL/Clair3 | ||
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| Basic information on how to use this tool: | ||
| - executable: run_clair3.sh | ||
| - help: -h, --help | ||
| - version: -v, --version | ||
| - description: <tool does something> | ||
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| Additional information: | ||
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| This container includes models in `/clair3/models` | ||
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| Full documentation: https://github.com/HKU-BAL/Clair3 | ||
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| ## Example Usage | ||
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| ```bash | ||
| run_clair3.sh \ | ||
| --bam_fn=${BAM} \ | ||
| --ref_fn=${REF} \ | ||
| --threads=${THREADS} \ | ||
| --platform="ont" \ ## options: {ont,hifi,ilmn} | ||
| --model_path=${MODEL_PREFIX} \ ## absolute model path prefix | ||
| --output=${OUTPUT_DIR} ## absolute output path prefix | ||
| ## pileup output file: ${OUTPUT_DIR}/pileup.vcf.gz | ||
| ## full-alignment output file: ${OUTPUT_DIR}/full_alignment.vcf.gz | ||
| ## Clair3 final output file: ${OUTPUT_DIR}/merge_output.vcf.gz | ||
| ``` |