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add docker resources
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Michael-Geuenich committed Jun 2, 2023
1 parent 8950545 commit 8475c00
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17 changes: 17 additions & 0 deletions Dockerfile
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FROM bioconductor/bioconductor_docker:RELEASE_3_16-R-4.2.3

ADD scripts/install_R_packages.R /tmp/install_R_packages.R
RUN Rscript /tmp/install_R_packages.R

# Install Python 3
RUN apt-get update && apt-get install -y python3

# Install pip for Python 3
RUN apt-get install -y python3-pip

# Install Python packages
RUN pip3 install numpy pandas sklearn joblib

RUN ln -s /usr/bin/python3 /usr/bin/python

RUN git clone --depth 1 https://github.com/tidyverse/ggplot2.git
30 changes: 30 additions & 0 deletions scripts/install_R_packages.R
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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'
)

ip <- installed.packages()
packages <- packages[!(packages %in% rownames(ip))]

BiocManager::install(packages)

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