koetjen/rstudio repository overview

koetjen/rstudio:seurat5

FROM ghcr.io/washu-it-ris/rstudio:4.3.0

ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
ARG DEBIAN_FRONTEND=noninteractive
RUN apt-get update --fix-missing && apt-get install -y build-essential libcurl4-openssl-dev libxml2-dev libhdf5-dev curl libssl-dev libxml2-dev git python3 jags libfontconfig1-dev r-cran-rjags time && apt-get clean

RUN R -e "install.packages(c('remotes','BiocManager','rsvd'), repo = 'https://cran.wustl.edu/⁠' , dependencies=TRUE)"
RUN R -e "BiocManager::install(c('hexbin','SummarizedExperiment','glmGamPoi'), ask = FALSE)"
RUN R -e "install.packages('BPCells', repo = 'https://bnprks.r-universe.dev/⁠', dependencies=TRUE); install.packages('presto', repo = 'https://satijalab.r-universe.dev⁠', dependencies=TRUE)"
RUN R -e "remotes::install_github('satijalab/seurat', ref = 'develop', quiet = TRUE, upgrade = TRUE); remotes::install_github('mojaveazure/seurat-disk', quiet = TRUE, upgrade = TRUE); BiocManager::install(c('clusterProfiler','enrichplot','msigdbr','org.Hs.eg.db'), ask = FALSE)"

koetjen/rstudio:seurat5_devtools

FROM koetjen/rstudio:seurat5

ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
ARG DEBIAN_FRONTEND=noninteractive
RUN apt-get update --fix-missing && apt-get install -y libudunits2-dev cmake libgsl-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev gdal-bin libgdal-dev libcairo2-dev && apt-get clean

RUN R -e "BiocManager::install(c('infercnv','ComplexHeatmap','dittoSeq','DropletUtils','Nebulosa'), ask = FALSE)"
RUN R -e "remotes::install_github(c('cole-trapnell-lab/monocle3', 'satijalab/azimuth'), upgrade = TRUE)"
RUN R -e "install.packages(c('Signac','ggpubr','rliger','scCustomize','tidyverse','devtools'), repo = 'https://cran.wustl.edu/⁠', dependencies=TRUE)"
RUN R -e "options(timeout=300); remotes::install_github('satijalab/seurat-wrappers')"