Olamide Isreal
9e6a16c19b
Large reference/model files excluded from repo - to be staged to S3 or baked into Docker images.
97 lines
2.7 KiB
Plaintext
97 lines
2.7 KiB
Plaintext
#FROM nvidia/cuda:12.2.2-cudnn8-runtime-ubuntu22.04
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FROM rust:1.61
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USER root
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SHELL ["/bin/bash", "-c"]
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#SHELL [ "/bin/sh", "-s", ".", "$HOME/.cargo/env" ]
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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 software-properties-common --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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ca-certificates \
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libopenblas-dev \
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libgsl-dev \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*
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# Get Rust
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#RUN curl https://sh.rustup.rs -sSf | bash -s -- --default-toolchain nightly -y
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#RUN source $HOME/.cargo/env
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#RUN echo 'source $HOME/.cargo/env' >> $HOME/.bashrc
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# Install vcf2prot
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RUN git clone https://github.com/ikmb/vcf2prot.git
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WORKDIR /home/omic/vcf2prot
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RUN cargo build --release
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WORKDIR /home/omic/vcf2prot/target/release
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RUN export DEBUG_CPU_EXEC=TRUE
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RUN export INSPECT_TXP=TRUE
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RUN export INSPECT_INS_GEN=TRUE
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#Test
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RUN ./vcf2prot -h
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WORKDIR /home/omic/vcf2prot
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RUN gunzip examples/reference_sequences.fasta.gz
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COPY reference.fasta .
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#install bcftools
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WORKDIR /home/omic/
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# install conda
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RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh && \
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mkdir -p /opt && \
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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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## update conda
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RUN conda update -y -n base -c defaults conda
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# main conda env (vcf2prot)
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RUN conda create -n vcf2prot python=3.9
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ENV PATH "$PATH:/opt/conda/envs/vcf2prot/bin"
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RUN echo "source activate vcf2prot" >> ~/.bashrc
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RUN conda install -y -n vcf2prot -c bioconda openssl
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RUN conda install -y -n vcf2prot -c conda-forge libgcc-ng
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RUN conda install -y -n vcf2prot -c bioconda bcftools==1.20
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#Install beagle
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#RUN wget https://faculty.washington.edu/browning/beagle/beagle.28Jun21.220.jar
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#Get data
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RUN wget https://ftp.ensembl.org/pub/release-112/gff3/homo_sapiens/Homo_sapiens.GRCh38.112.gff3.gz
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RUN gunzip Homo_sapiens.GRCh38.112.gff3.gz
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#RUN wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
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#RUN gunzip hg38.fa.gz
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RUN wget https://ftp.ensembl.org/pub/release-112/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz
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RUN gunzip Homo_sapiens.GRCh38.dna.toplevel.fa.gz
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WORKDIR /home/omic/vcf2prot
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RUN conda install -y -n vcf2prot numpy pandas
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COPY MANE_transcipts_reference.fasta .
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