Using Rstudio with mamba-installed R

__1. Download and unzip Rstudio Tarball

• Download tarball from : https://posit.co/download/rstudio-desktop/
  • I downloaded the following tarball for my CentOS 7 server
• Unzip the tarball and change the owner and mode of chrome-sandbox

  • tar -zxf rstudio-2023.09.0-463-x86_64-fedora.tar.gz
    cd rstudio-2023.09.0+463
    # the following 2 commands are from the error message that shows up after executing rstudio right after the tarball unzipping.
    sudo chown root:root chrome-sandbox
    sudo chmod 4755 chrome-sandbox
    ls -l chrome-sandbox
    #-rwsr-xr-x. 1 root root 53840  Sep 26 09:16 chrome-sandbox
    

__2. Download R using Conda or Mambaforge

• I prefer to use conda/mamba to install R and R packages for easy installation and compatibility.
• Mambaforge is better than plain conda nowadays because of the speed of package resolution and installation.
• How to install and setup mambaforge : https://github.com/conda-forge/miniforge
• create a conda environment and at the same time install R and R packages using mamba

  • mamba create -n cosmx -c conda-forge -c r -c bioconda r-base  r-seurat r-devtools r-terra r-magick
    

__3. Environment Modules to easily set pathes

• In order for Rstudio to recognize the R installed using conda/mamba, we need to set PATH,LD_LIBRARY_PATH, and CPATH (I haven’t tested whether setting CPATH is essential or not)
• The Enviroment Modules package makes it easy to dynamically load and unload those path settings.
• Install Environment Modules : https://modules.readthedocs.io/en/stable/INSTALL.html
  • install tcl and tcl-devel if not already before installation.

    • yum install tcl tcl-devel
      

  • Download and install module files as described in the link : https://modules.readthedocs.io/en/stable/INSTALL.html
  • To use modulefile you need to source the profile. For me, I put it in the ~/.bashrc. I also set my custom MODULEPATH where modulefiles are stored.

    • #~/.bashrc
      source /usr/local/Modules/init/profile.sh
      export MODULEPATH=${MODULEPATH}:/home/hd00ljy/modulefiles/tools
      

  • make a modulefile

    • nano modulefiles/tools/cosmx/1
      

    • #%Module1.0
      
      proc ModulesHelp { } {
          puts stderr "              "
          puts stderr "\tThis module is for use of [module-info name]."
          puts stderr "              "
          puts stderr "\tYou need module(s): "
          puts stderr "\t              none "
          puts stderr "\tuse example: "
          puts stderr "\t    $ module load [module-info name]"
          puts stderr "              "
      }
      
      # install history
      #################################
      #mamba create -n cosmx -c conda-forge -c r -c bioconda r-base  r-seurat r-devtools r-terra r-magick
      #################################
      
      
      #if { [ module-info mode load ] } {
      #    module load gcc/7.4.0
      #}
      
      
      module-whatis   "loads the modules environment"
      
      # for Tcl script use only
      set      name            cosmx
      set      version         4.3.1
      set      envdir          /home/hd00ljy/mambaforge/envs
      set      prefix          $envdir/$name
      
      #if {![file exists $prefix]} {
      #    puts stderr "\t[module-info name] Load Error: $prefix does not exist"
      #    break
      #    exit 1
      #}
      
      prepend-path    PATH              $prefix/bin
      prepend-path    LD_LIBRARY_PATH   $prefix/lib/R/lib
      prepend-path    CPATH             $prefix/lib/R/include
      prepend-path    LD_LIBRARY_PATH   $prefix/lib
      prepend-path    CPATH             $prefix/include
      
      
      #if { [ module-info mode remove ] || [ module-info mode switch ]  } {
      #        module unload gcc/7.4.0
      #}
             
      

• you can now load and unload conda-installed R(executables,libraries, and headers) using module command

  • module load cosmx/1 # load module
    module purge # unload all modules that have been loaded
    

__4. Execute Rstudio

• load module for conda/mamba-installed R

  • module load cosmx/1 # load module
    

• Launch Rstudio

  • cd rstudio-2023.09.0+463
    ./rstudio