Create docker-image.yml

.github/workflows/docker-image.yml

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+FROM rocker/rstudio:4.0.3
+
+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 xorg openbox
+  && 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)"]