# Start from the RStudio base image

FROM rocker/rstudio:latest

# dependencies

RUN apt-get update

RUN apt-get install -y libgdal-dev libfftw3-dev libmagick++-dev cmake libhdf5-dev git libopencv-dev libopencv-features2d-dev  

RUN apt-get install -y libssl-dev libcurl4-openssl-dev libgit2-dev libxml2-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev libz-dev

# OpenCV

RUN wget https://github.com/opencv/opencv/archive/refs/tags/4.8.1.zip

RUN unzip 4.8.1.zip

RUN rm 4.8.1.zip

RUN wget https://github.com/opencv/opencv_contrib/archive/refs/tags/4.8.1.zip

RUN unzip 4.8.1.zip

RUN rm 4.8.1.zip

RUN mkdir build

WORKDIR "build"

RUN cmake -D CMAKE_BUILD_TYPE=RELEASE -D CMAKE_INSTALL_PREFIX=/usr/local -D INSTALL_C_EXAMPLES=ON -D INSTALL_PYTHON_EXAMPLES=ON  -D OPENCV_GENERATE_PKGCONFIG=ON -D OPENCV_EXTRA_MODULES_PATH=../opencv_contrib-4.8.1/modules/  -D BUILD_opencv_xfeatures2d=ON ../opencv-4.8.1/

RUN make -j5

RUN make install

RUN sh -c 'echo "/usr/local/lib" > /etc/ld.so.conf.d/opencv.conf'

RUN ldconfig

# Install required R packages

RUN R -e "install.packages(c('shiny', 'devtools', 'BiocManager'), repos='http://cran.rstudio.com/')"

# Install VoltRon dependencies

RUN R -e "install.packages(c('grDevices', 'data.table', 'RcppAnnoy', 'RANN', 'Matrix', 'dplyr', 'ggplot2', 'ggrepel', 'igraph', 'irlba', 'rjson', 'magick', 'ids', 'sp', 'reshape2', 'rlang', 'ggpubr', 'shinyjs'), repos='http://cran.rstudio.com/')"

RUN R -e "install.packages(c('stringr', 'uwot', 'RCDT'), repos='http://cran.rstudio.com/')"

RUN R -e "BiocManager::install(c('EBImage', 'S4Arrays'))"

# Install Suggested dependencies

RUN R -e "BiocManager::install(c('DelayedArray'))"

RUN R -e "BiocManager::install(c('HDF5Array'))"

RUN R -e "remotes::install_github('bnprks/BPCells/r@v0.3.0')"

RUN R -e "remotes::install_github('BIMSBbioinfo/ImageArray')"

RUN R -e "remotes::install_github('BIMSBbioinfo/HDF5DataFrame')"

RUN R -e "remotes::install_github('BIMSBbioinfo/ZarrDataFrame')"

RUN R -e "install.packages('Seurat')"

RUN R -e "BiocManager::install('glmGamPoi')"

RUN R -e "install.packages('arrow')"

RUN R -e "BiocManager::install('RBioFormats')"

RUN R -e "BiocManager::install('ComplexHeatmap')"

RUN R -e "devtools::install_github('xuranw/MuSiC')"

RUN R -e "BiocManager::install('SingleCellExperiment')"

RUN R -e "BiocManager::install('SpatialExperiment')"

RUN R -e "install.packages('dplyr')"

RUN R -e "BiocManager::install('DESeq2')"

RUN R -e "install.packages('ggnewscale')"

RUN R -e "install.packages('patchwork')"

RUN R -e "install.packages('anndata')"

RUN R -e "install.packages('R.utils')"

RUN R -e "devtools::install_github('immunogenomics/presto')"

# Install VoltRon dependencies

RUN R -e "devtools::install_github('Artur-man/VoltRon')"

# Install basilisk and setup environment

USER rstudio

RUN R -e "BiocManager::install('basilisk')"

RUN R -e "basilisk::obtainEnvironmentPath(VoltRon::getBasilisk())"

RUN sh -c 'echo "options(voltron.python.path = \"/home/rstudio/.cache/R/basilisk/1.18.0/VoltRon/0.2.0/VoltRon_basilisk_env/bin/python\")" > /home/rstudio/.Rprofile'

# set up java

USER root

RUN apt-get update -y

RUN apt upgrade -y

RUN apt-get install -y openjdk-21-jdk

RUN export JAVA_HOME=/usr/lib/jvm/java-21-openjdk-arm64/

RUN R CMD javareconf -e

# Install java based packages

RUN R -e "install.packages('rJava')"

RUN R -e "BiocManager::install('RBioFormats')"

RUN sh -c 'echo "options(java.parameters = \"-Xmx10g\")" >> /home/rstudio/.Rprofile'

# Install spacexr

RUN apt-get install -y libgsl-dev

RUN R -e "options(timeout = 600000000); devtools::install_github(\"dmcable/spacexr\")"

# increase cache disk size for ImageMagick

RUN sed -i 's/2GiB/10GiB/g' /etc/ImageMagick-6/policy.xml

# vitessceR

RUN apt-get update -y

RUN apt upgrade -y

RUN apt-get install -y libsodium-dev 

RUN R -e "options(timeout = 600000000); devtools::install_github(\"vitessce/vitessceR\")"