Olamide Isreal
9e6a16c19b
Large reference/model files excluded from repo - to be staged to S3 or baked into Docker images.
127 lines
3.5 KiB
Plaintext
127 lines
3.5 KiB
Plaintext
# Start with Ubuntu base
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FROM ubuntu:22.04
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USER root
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SHELL ["/bin/bash", "-c"]
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# Set environment variables
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ENV DEBIAN_FRONTEND=noninteractive \
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TZ=Etc/UTC \
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PATH="/opt/conda/bin:/opt/conda/condabin:/opt/conda/envs/ecotyper/bin:$PATH" \
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R_LIBS="/opt/conda/envs/ecotyper/lib/R/library:/ecotyper/R/library" \
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ECOTYPER_HOME="/ecotyper"
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# Install system dependencies
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RUN apt-get update && apt-get install -y --no-install-recommends \
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wget \
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ca-certificates \
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git \
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libcurl4-openssl-dev \
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libssl-dev \
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libxml2-dev \
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build-essential \
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r-base \
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r-base-dev \
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libcairo2-dev \
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libxt-dev \
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libgraphicsmagick1-dev \
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default-jdk \
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xvfb \
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xauth \
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xfonts-base \
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&& rm -rf /var/lib/apt/lists/*
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# Set up R environment
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RUN echo "options(repos = c(CRAN = 'https://cloud.r-project.org'))" > /root/.Rprofile
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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 and create environment
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RUN conda update -y -n base -c defaults conda && \
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conda create -n ecotyper -c conda-forge -c bioconda \
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python=3.8 \
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r-base=4.1.3 \
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r-matrix \
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r-mass \
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r-nmf \
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r-rcpp \
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r-data.table \
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r-reshape2 \
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r-plyr \
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r-stringr \
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r-ggplot2 \
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r-rcolorbrewer \
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r-circlize \
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r-cowplot \
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r-viridis \
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r-gridextra \
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r-ggpubr \
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r-cluster \
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r-matrixtests \
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r-doparallel \
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r-foreach \
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r-optparse \
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r-argparse \
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r-config \
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r-colorspace \
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r-rjson \
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bioconductor-biobase \
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bioconductor-complexheatmap \
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bioconductor-genomicranges \
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-y && \
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conda clean -afy
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# Clone EcoTyper and setup directory structure
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RUN git clone --depth 1 https://github.com/digitalcytometry/ecotyper.git /ecotyper && \
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cd /ecotyper && \
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mkdir -p EcoTyper/Carcinoma/Carcinoma_Fractions/Analysis/rank_selection && \
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mkdir -p EcoTyper/Lymphoma/Lymphoma_Fractions/Analysis/rank_selection && \
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mkdir -p EcoTyper/Carcinoma/Carcinoma_Fractions/Cell_States/recovery && \
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mkdir -p EcoTyper/Carcinoma/Carcinoma_Fractions/Ecotypes/recovery && \
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mkdir -p EcoTyper/Lymphoma/Lymphoma_Fractions/Cell_States/recovery && \
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mkdir -p EcoTyper/Lymphoma/Lymphoma_Fractions/Ecotypes/recovery && \
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chmod -R +x pipeline/*.R && \
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chmod -R +x *.R
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# Setup EcoTyper permissions
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RUN cd /ecotyper && \
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ln -sf /ecotyper/pipeline pipeline && \
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chmod -R 755 /ecotyper/EcoTyper && \
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chmod -R 755 /ecotyper/pipeline
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# Setup CIBERSORTx
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RUN mkdir -p /src
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WORKDIR /src
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# Copy CIBERSORTx files
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COPY ./CIBERSORTx-fractionshires/ /src/
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# Install R dependencies for CIBERSORTx
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RUN R -e "if (!require('BiocManager', quietly=TRUE)) install.packages('BiocManager', repos='https://cloud.r-project.org/')" && \
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Rscript /src/install_R_dependencies.R
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# Add src to PATH
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ENV PATH="/src:${PATH}"
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# Setup final environment
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RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
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echo "conda activate ecotyper" >> ~/.bashrc
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#Add pandas
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RUN conda install -n ecotyper anaconda::pandas
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# Set default command
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CMD ["/bin/bash"]
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