Olamide Isreal
9e6a16c19b
Large reference/model files excluded from repo - to be staged to S3 or baked into Docker images.
50 lines
1.6 KiB
Plaintext
50 lines
1.6 KiB
Plaintext
FROM r-base:latest
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WORKDIR /usr/src/app
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# Install system dependencies
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RUN apt-get update && apt-get install -y \
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git \
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libcurl4-gnutls-dev \
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libssl-dev \
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libxml2-dev \
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procps # Adding procps for the 'ps' command
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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:$PATH
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RUN conda update -y -n base -c defaults conda
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# main conda env (rpy2)
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RUN conda create -n rpy2 python=3.9
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ENV PATH "$PATH:/opt/conda/envs/rpy2/bin"
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RUN echo "source activate rpy2" >> ~/.bashrc
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RUN conda clean --all -f -y
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RUN conda install -y -n rpy2 -c anaconda pandas
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RUN conda install -y -n rpy2 -c anaconda numpy
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# Install R packages
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RUN Rscript -e "install.packages('remotes', dependencies=TRUE)" \
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&& Rscript -e "remotes::install_github('federicogiorgi/corto')" \
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&& Rscript -e "install.packages('data.table', dependencies=TRUE)" \
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&& Rscript -e "install.packages('BiocManager')" \
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&& Rscript -e "BiocManager::install('DESeq2')"
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# Test commands to validate installation
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RUN Rscript -e "library(corto)"
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# Clone the corto repository (optional, based on your needs)
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RUN git clone https://github.com/federicogiorgi/corto.git
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CMD ["/bin/bash"]
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