Olamide Isreal
9e6a16c19b
Large reference/model files excluded from repo - to be staged to S3 or baked into Docker images.
93 lines
3.5 KiB
Plaintext
93 lines
3.5 KiB
Plaintext
FROM nvidia/cuda:12.2.2-cudnn8-runtime-ubuntu22.04
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USER root
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SHELL ["/bin/bash", "-c"]
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WORKDIR /home
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RUN mkdir -p /home/omic
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WORKDIR /home/omic
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ARG DEBIAN_FRONTEND=noninteractive
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RUN apt-get update -y && apt-get install -y --no-install-recommends \
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build-essential \
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cmake \
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curl \
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git \
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wget \
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cuda-toolkit-12-2 \
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ca-certificates \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*
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RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh \
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&& bash miniconda.sh -b -p /opt/conda \
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&& rm miniconda.sh \
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&& ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh \
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&& echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc \
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&& echo "conda activate base" >> ~/.bashrc \
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&& find /opt/conda/ -follow -type f -name '*.a' -delete \
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&& find /opt/conda/ -follow -type f -name '*.js.map' -delete \
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&& /opt/conda/bin/conda clean -afy
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ENV PATH /opt/conda/bin:$PATH
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# main conda env (borzoi)
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RUN conda create -n borzoi python=3.9
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ENV PATH "$PATH:/opt/conda/envs/borzoi/bin"
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RUN echo "source activate borzoi" >> ~/.bashrc
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RUN conda clean --all -f -y
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# Install borzoi
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RUN git clone https://github.com/calico/baskerville.git
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WORKDIR /home/omic/baskerville
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RUN /opt/conda/envs/borzoi/bin/python3 -m pip install -e .
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WORKDIR /home/omic
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RUN git clone https://github.com/calico/borzoi.git
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WORKDIR /home/omic/borzoi
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RUN /opt/conda/envs/borzoi/bin/python3 -m pip install -e .
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# Install pretrained models
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RUN mkdir -p /home/omic/borzoi/saved_models
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WORKDIR /home/omic/borzoi/saved_models
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RUN mkdir -p f0 && mkdir -p f1 && mkdir -p f2 && mkdir -p f3
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RUN wget --no-check-certificate -O /home/omic/borzoi/saved_models/f0/model0_best.h5 https://storage.googleapis.com/seqnn-share/borzoi/f0/model0_best.h5
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RUN wget --no-check-certificate -O /home/omic/borzoi/saved_models/f1/model0_best.h5 https://storage.googleapis.com/seqnn-share/borzoi/f1/model0_best.h5
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RUN wget --no-check-certificate -O /home/omic/borzoi/saved_models/f2/model0_best.h5 https://storage.googleapis.com/seqnn-share/borzoi/f2/model0_best.h5
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RUN wget --no-check-certificate -O /home/omic/borzoi/saved_models/f3/model0_best.h5 https://storage.googleapis.com/seqnn-share/borzoi/f3/model0_best.h5
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WORKDIR /home/omic/borzoi
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# Get hg38
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RUN wget -O - https://hgdownload2.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz | gunzip -c > hg38.fa
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# Get other supporting data
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RUN wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_nort.gtf.gz | gunzip -c > gencode41_basic_nort.gtf
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RUN wget https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_protein_splice.csv.gz
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RUN wget https://storage.googleapis.com/seqnn-share/helper/polyadb_human_v3.csv.gz
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# Index the reference
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RUN /opt/conda/envs/borzoi/bin/python3 -m pip install pyfaidx
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RUN /opt/conda/envs/borzoi/bin/python3 -c "import pyfaidx; pyfaidx.Faidx('hg38.fa')"
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#Install samtools
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RUN apt-get update -y && apt-get install -y libz-dev liblzma-dev libbz2-dev libcurl4-gnutls-dev
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WORKDIR /home/omic
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RUN git clone --recurse-submodules https://github.com/samtools/htslib.git
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RUN git clone https://github.com/samtools/bcftools.git
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WORKDIR /home/omic/bcftools
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# The following is optional:
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#RUN autoheader && autoconf && ./configure --enable-libgsl --enable-perl-filters
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RUN make
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RUN export BCFTOOLS_PLUGINS=/home/omic/bcftools
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WORKDIR /home/omic/borzoi
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COPY ncbiRefSeq_bigger.csv .
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COPY ncbiRefSeq_subset.pickle .
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#copy MANE data
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COPY prot_bigger.csv .
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COPY prot_subset.pickle .
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COPY TPM_NO_MUTATIONS.csv .
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# test
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