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FROM bioconductor/bioconductor_docker:RELEASE_3_16-R-4.2.3 | ||
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ADD scripts/install_R_packages.R /tmp/install_R_packages.R | ||
RUN Rscript /tmp/install_R_packages.R | ||
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# Install Python 3 | ||
RUN apt-get update && apt-get install -y python3 | ||
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# Install pip for Python 3 | ||
RUN apt-get install -y python3-pip | ||
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# Install Python packages | ||
RUN pip3 install numpy pandas sklearn joblib | ||
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RUN ln -s /usr/bin/python3 /usr/bin/python | ||
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RUN git clone --depth 1 https://github.com/tidyverse/ggplot2.git |
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packages <- c( | ||
'tidyverse', | ||
'RColorBrewer', | ||
'patchwork', | ||
'caret', | ||
'SingleCellExperiment', | ||
'splitstackshape', | ||
'fabricatr', | ||
'scmap', | ||
'SingleR', | ||
'Seurat', | ||
'yaml', | ||
'glue', | ||
'scater', | ||
'yardstick', | ||
'data.table', | ||
'scales', | ||
'ComplexHeatmap', | ||
'circlize', | ||
'viridis', | ||
'ggalluvial', | ||
'magick', | ||
'ggpubr', | ||
'broom' | ||
) | ||
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ip <- installed.packages() | ||
packages <- packages[!(packages %in% rownames(ip))] | ||
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BiocManager::install(packages) |