Olamide Isreal
9e6a16c19b
Large reference/model files excluded from repo - to be staged to S3 or baked into Docker images.
65 lines
2.1 KiB
Plaintext
65 lines
2.1 KiB
Plaintext
FROM ubuntu:latest
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ARG DEBIAN_FRONTEND=noninteractive
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USER root
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# Install gradle and JDK
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RUN apt -y update && apt-get -y update
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RUN apt install -y build-essential openjdk-8-jdk wget git python3 python3-pip tabix
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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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sh 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:$PATH
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# main conda env (synthea)
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RUN conda create -n synthea
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ENV PATH "$PATH:/opt/conda/envs/synthea/bin"
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RUN echo "source activate synthea" >> ~/.bashrc
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# Install pandas and numpy
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RUN python3 -m pip install --upgrade pip
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RUN python3 -m pip install pandas numpy fuzzywuzzy python-Levenshtein requests
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# Install synthea from latest release
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RUN wget https://github.com/synthetichealth/synthea/archive/refs/tags/master-branch-latest.tar.gz
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RUN tar xzf master-branch-latest.tar.gz && mv synthea-master-branch-latest synthea
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WORKDIR /synthea
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ARG PATH $PATH:/synthea
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ENV PATH $PATH:/synthea
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RUN conda config --add channels bioconda
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RUN conda config --add channels conda-forge
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# Install samtools
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RUN conda install -n synthea -c bioconda samtools
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# Install UCSC Liftover
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RUN conda install -n synthea -c bioconda ucsc-liftover
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RUN conda install -n synthea -c bioconda gatk4
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RUN conda install -n synthea -c bioconda bedtools
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RUN apt-get -y install vcftools
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# DNA to Protein Sequence code
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WORKDIR /synthea
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RUN git clone https://github.com/prestevez/dna2proteins.git
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RUN mv dna2proteins/dna2proteins.py .
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RUN rm -r dna2proteins
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RUN apt install -y 2to3
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RUN 2to3 -w dna2proteins.py
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#Test
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# RUN ./gradlew build check test
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RUN ./run_synthea -p 10 --exporter.csv.export true
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# use -a for age range e.g. 30-40 and -g for gender M/F
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