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Update docker-image.yml #2

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FROM rocker/rstudio:4.0.3

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MAINTAINER Aussel Rudy ([email protected])
# ##############################
# R packages system dependencies
# ##############################
RUN apt-get update && apt-get install -y optipng \
pandoc \
libpng-dev \
zlib1g-dev \
libssl-dev \
libcurl4-openssl-dev \
libglpk-dev
# ####################################
# INSTALLING R PACKAGES FOR PROJECT
# ####################################
RUN apt-get update && apt-get install -y libudunits2-dev imagemagick libhdf5-dev libxml2-dev zlib1g-dev
RUN apt-get update \
&& export DEBIAN_FRONTEND=noninteractive \
&& apt-get -y install libx11-dev freeglut3 freeglut3-dev libpng-dev
RUN R -e 'install.packages( "ade4")'
RUN R -e 'install.packages( "BiocManager")'
RUN R -e 'install.packages( "checkmate")'
RUN R -e 'install.packages( "cowplot")'
RUN R -e 'install.packages( "data.table")'
RUN R -e 'install.packages( "devtools")'
RUN R -e 'install.packages( "dplyr")'
RUN R -e 'install.packages( "DT")'
RUN R -e 'install.packages( "ggplot2")'
RUN R -e 'install.packages( "ggrepel")'
RUN R -e 'install.packages( "ggridges")'
RUN R -e 'install.packages( "ggsignif")'
RUN R -e 'install.packages( "gplots")'
RUN R -e 'install.packages( "gridExtra")'
RUN R -e 'install.packages( "igraph")'
RUN R -e 'install.packages( "htmltools")'
RUN R -e 'install.packages( "heatmaply")'
RUN R -e 'install.packages( "knitr")'
RUN R -e 'install.packages( "magrittr")'
RUN R -e 'install.packages( "matrixStats")'
RUN R -e 'install.packages( "pheatmap")'
RUN R -e 'install.packages( "plotly")'
RUN R -e 'install.packages( "Rcpp")'
RUN R -e 'install.packages( "RColorBrewer")'
RUN R -e 'install.packages( "reshape")'
RUN R -e 'install.packages( "Rgraphviz")'
RUN R -e 'install.packages( "rmarkdown")'
RUN R -e 'install.packages( "rprojroot")'
RUN R -e 'install.packages( "Rtsne")'
RUN R -e 'install.packages( "shiny")'
RUN R -e 'install.packages( "shinyBS")'
RUN R -e 'install.packages( "shinydashboard")'
RUN R -e 'install.packages( "stringr")'
RUN R -e 'install.packages( "sp")'
RUN R -e 'install.packages( "tools")'
RUN R -e 'install.packages( "umap")'
RUN R -e 'install.packages( "utils")'
RUN R -e 'install.packages( "viridis")'
RUN R -e 'library(devtools);devtools::install_github("JinmiaoChenLab/Rphenograph")'
RUN R -e 'library(devtools);devtools::install_github("JinmiaoChenLab/ClusterX")'
RUN R -e 'library(devtools);devtools::install_github("romanhaa/cerebroApp")'
RUN R -e 'BiocManager::install("flowCore")'
RUN R -e 'BiocManager::install("openCyto")'
RUN R -e 'BiocManager::install("CytoML")'
RUN R -e 'BiocManager::install("flowViz")'
RUN R -e 'BiocManager::install("flowWorkspace")'
RUN R -e 'BiocManager::install("ggcyto")'
RUN R -e 'BiocManager::install("flowUtils")'
RUN R -e 'BiocManager::install()'
RUN R -e 'library(BiocManager)'
RUN R -e 'install.packages( "BiocManager")'
RUN R -e 'install.packages("BiocInstaller")'
RUN R -e 'BiocManager::install("multtest")'
RUN R -e 'install.packages("remotes")'
RUN R -e 'remotes::install_version("SDMTools", "1.1-221")'
RUN R -e 'install.packages("Seurat")'
RUN R -e 'install.packages( "sctransform")'
RUN R -e 'library(devtools);devtools::install_github("rstudio/DT")'
RUN R -e 'install.packages("DDRTree")'
RUN R -e 'install.packages("pheatmap")'
RUN R -e 'install.packages("shinyFiles")'
RUN R -e 'install.packages("shinybusy")'
RUN R -e 'install.packages("shinycssloaders")'
RUN R -e 'install.packages("pheatmap")'
RUN R -e 'install.packages("corrplot")'
RUN R -e 'install.packages("shinywidgets")'
RUN R -e 'install.packages("dplyr", dependencies = TRUE)'
RUN R -e 'BiocManager::install("biomaRt")'
RUN R -e 'install.packages("shinyWidgets")'
RUN R -e 'install.packages("shinyalert")'
RUN R -e 'install.packages("stringr")'
RUN apt-get update
RUN apt-get install build-essential chrpath libssl-dev libxft-dev -y
RUN apt-get install libfreetype6 libfreetype6-dev -y
RUN apt-get install libfontconfig1 libfontconfig1-dev -y
RUN cd ~
RUN wget https://github.com/Medium/phantomjs/releases/download/v2.1.1/phantomjs-2.1.1-linux-x86_64.tar.bz2
RUN tar xvjf phantomjs-2.1.1-linux-x86_64.tar.bz2
RUN mv phantomjs-2.1.1-linux-x86_64 /usr/local/share
RUN ln -sf /usr/local/share/phantomjs-2.1.1-linux-x86_64/bin/phantomjs /usr/local/bin
RUN R -e 'install.packages("webshot")'
RUN apt-get install -y python3-pip
RUN apt-get install -y software-properties-common
RUN apt-get update && apt-get install -y gnupg
RUN wget -O - https://apt.kitware.com/keys/kitware-archive-latest.asc 2>/dev/null | apt-key add -
RUN apt-add-repository 'deb https://apt.kitware.com/ubuntu/ bionic main'
RUN apt-get update && apt-get install -y cmake
RUN pip3 install numpy
RUN pip3 install leidenalg
COPY Reference/leiden_0.3.10.tar.gz /
#RUN R -e 'devtools::install_github("TomKellyGenetics/leiden")'
RUN R -e 'install.packages( "/leiden_0.3.10.tar.gz", repos = NULL, type = "source")'
RUN R -e 'install.packages("kableExtra")'
RUN R -e 'BiocManager::install("org.Mm.eg.db")'
RUN R -e 'BiocManager::install("clusterProfiler")'
RUN R -e 'BiocManager::install("org.Hs.eg.db")'
# copy the app to the image
RUN mkdir /root/Shiva
COPY Shiva /root/Shiva
RUN ls -la /root/Shiva/*
COPY Reference/Rprofile.site /usr/lib/R/etc/
EXPOSE 3838
# ####################################
# CLEAN INSTALL
# ####################################
RUN apt-get clean\
&& apt-get remove --yes --purge build-essential
RUN mkdir -p /mnt
CMD ["R", "-e", "shiny::runApp(appDir = '/root/Shiva', host='0.0.0.0', port=3838)"]