<commit_before># Build with:
#   sudo docker build -t deepconsensus .
# For GPU:
#   sudo docker build --build-arg build_gpu=true --build-arg FROM_IMAGE=nvidia/cuda:11.3.0-cudnn8-runtime -t deepconsensus_gpu .



ARG FROM_IMAGE=continuumio/miniconda3

FROM continuumio/miniconda3 as conda_setup
RUN conda config --add channels defaults && \
    conda config --add channels bioconda && \
    conda config --add channels conda-forge
RUN conda create -n bio \
                    python=3.8 \
                    pbcore \
                    pbbam \
                    pbccs \
                    pbmm2 \
                    parallel \
                    jq \
                    gcc \
                    pycocotools \
                    bioconda::seqtk \
                    bioconda::unimap \
                    bioconda::bedtools \
                    bioconda::minimap2 \
                    bioconda::extracthifi \
                    bioconda::zmwfilter \
                    bioconda::pysam \
                    bioconda::samtools=1.10 \
                    bioconda::pyfastx=0.8.4 \
    && conda clean -a
RUN wget https://github.com/PacificBiosciences/align-clr-to-ccs/releases/download/0.2.0/actc && \
    chmod +x actc && \
    mv actc /opt/conda/bin/<commit_msg>Internal Updates<commit_after># Build with:
#   sudo docker build -t deepconsensus .
# For GPU:
#   sudo docker build --build-arg build_gpu=true --build-arg FROM_IMAGE=nvidia/cuda:11.3.0-cudnn8-runtime -t deepconsensus_gpu .



ARG FROM_IMAGE=continuumio/miniconda3

FROM continuumio/miniconda3 as conda_setup
RUN conda config --add channels defaults && \
    conda config --add channels bioconda && \
    conda config --add channels conda-forge
RUN conda create -n bio \
                    python=3.8 \
                    pbcore \
                    pbbam \
                    pbccs \
                    pbmm2 \
                    parallel \
                    jq \
                    gcc \
                    memory_profiler \
                    pycocotools \
                    bioconda::seqtk \
                    bioconda::unimap \
                    bioconda::bedtools \
                    bioconda::minimap2 \
                    bioconda::extracthifi \
                    bioconda::zmwfilter \
                    bioconda::pysam \
                    bioconda::samtools=1.10 \
                    bioconda::pyfastx=0.8.4 \
    && conda clean -a
RUN wget https://github.com/PacificBiosciences/align-clr-to-ccs/releases/download/0.2.0/actc && \
    chmod +x actc && \
    mv actc /opt/conda/bin/
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{'dir': 'git-commits-cleaned', 'id': '4167569', 'n_tokens_mistral': 829, 'n_tokens_neox': 754, 'n_words': 153}