On Virtual Box

If by any means you see that the installations are not working as it should on your computer, you can try to create a virtual machine to run UBUNTU and install everything there. But please keep this alternative as the last temporary resourse, as we recommend troubleshooting the installation o the up-mentioned methods.

  1. Download and install on your machine VIRTUALBOX https://www.virtualbox.org Links to an external site.

  2. Download the ISO disk of UBUNTU https://ubuntu.com/download/desktop Links to an external site.

  3. On VIRTUALBOX, click on Settings (yellow engine) > General > Advanced and make sure that both settings Shared Clipboard and Drag'n'Drop are set to Bidirectional.

  4. Completely close VIRTUALBOX and start it again to apply changes.

  5. On VIRTUALBOX, create a machine called Ubuntu and add the image above

  • set the memory to the maximum allowed in the GREEN bar
  • set the hard disk to be dynamic allocated
  • all other things can be default

  1. Proceed with the Ubuntu installation as recommended. You can set to do "Minimal Installation" and deactivate to get updates during installation.

  2. Inside Ubuntu, open TERMINAL and type the commands below to install the X-server graphical packages that will be used to launch RStudio. https://docs.anaconda.com/anaconda/install/linux/ Links to an external site.

  sudo apt-get update
  sudo apt-get install libgl1-mesa-glx libegl1-mesa libxrandr2 libxrandr2 libxss1 libxcursor1 libxcomposite1 libasound2 libxi6 libxtst6
  1. Inside UBUNTU, Download conda:
  wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
  1. Inside UBUNTU, open the TERMINAL and type the commands below. Follow the instructions for the installation there.
  cd ~/Downloads
  sh Miniconda3-latest-Linux-x86_64.sh
  1. Close Terminal to apply the CONDA updates. Then you can create a course folder, download the environment file and create the environment:
  mkdir ~/Desktop/course
  cd ~/Desktop/course
  wget https://raw.githubusercontent.com/NBISweden/workshop-scRNAseq/master/labs/environment_scRNAseq2021.yml
  conda env create -f environment_scRNAseq2021.yml
  1. You can then follow the instructions above to activate/deactivate the environment.
  conda activate scRNAseq2021
  rstudio &