Conda

During this workshop, you will use conda environments to run the exercises. This is because conda environments allow all users to have the same computing environment, i.e. package versions. This enforces reproducibility for you to run this material without the need to re-install or change your local versions. See and graphical example below:

Conda environments Links to an external site. are a self-contained directory that you can use in order to reproduce all your results.

Briefly, you need to:

  1. Install Conda
  2. Download the .yml environment file
  3. Create and activate the environment
  4. Deactivate the environment after running your analyses

You can read more Links to an external site. about Conda environments and other important concepts to help you make your research reproducible.

 

1. Download and install Conda and Mamba

Start by installing Conda. We suggest installing Miniconda3 and NOT Anaconda. After installing Conda Links to an external site..

On Mac OS X

First, make sure you have Xcode and CommandLineTools installed and updated to latest version (in AppStore). If you have not already installed CommadLineTools, go to a terminal window and run:

xcode-select --install

OBS! If you are on an M1 (Silicon) Mac computer you will have to use a Rosetta2 enabled terminal and install the x86_64 miniconda3 version. All R packages are not yet available as conda packages for the arm64 architecture.

Just right-click on the icon for the terminal app in a Finder window and click "Get Info". There you have a selection box: "Open using Rosetta" that you need to tick before opening the application.  Then you can install the x86_64 miniconda3 following instructions below.

First download the latest version of Miniconda3 and run it to install.

  curl -o Miniconda3-latest-MacOSX-x86_64.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
  sh Miniconda3-latest-MacOSX-x86_64.sh

Follow the instructions on screen, scrolling down, pressing ENTER and replying yes when necessary. Install it in the default directory. Restart your terminal window to apply modifications. After restarting, you can type the command below to install Mamba:

  conda init
  conda install -n base -c conda-forge mamba

 

On Ubuntu

First download the latest version of Miniconda3 and run it to install.

  wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
  sh Miniconda3-latest-Linux-x86_64.sh

Follow the instructions on screen replying yes when necessary. Restart your terminal window to apply modifications. After restarting, you can type the command below to install Mamba:

  conda init
  conda install -n base -c conda-forge mamba

 

On Windows 10

Unfortunately, not all packages available on conda are compatible with windows machines. The good news is that Windows 10 offers native linux support via the Windows Subsystem for Linux (WSL2). This allows you to run linux/bash commands from within windows without the need of a virtual machine nor a dual-boot setup (i.e. having 2 operating systems). However, WSL does not offer a complete support for graphical interfaces (such as RStudio in our case), so we need additional steps to make that happen.

  1. On Windows 10, install the WSL if you don't have it. Follow the instructions here: https://docs.microsoft.com/en-us/windows/wsl/install-win10 Links to an external site.

  2. Once you have that installed, you can download and install MobaXterm (which is the enhanced terminal with graphical capacity): https://mobaxterm.mobatek.net Links to an external site.
    It is recommended that you INSTALL the program and not use the portable version.

  3. Inside MobaXterm, you will probably will see that your WSL is already listed on the left panel as an available connection. Just double-click it and you will be accessing it via MobaXterm. If by any chance you don't see it there, close MobaXterm and go to the WSL terminal, because probably the WSL is not allowing SSH connections. You can follow this link Links to an external site. for the instructions on how to do it. You need to complete until the step Start or restart the SSH service, while the further steps are optional, but might be useful.

  4. Inside MobaXterm, download Conda with the command:

  wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
  1. Inside MobaXterm, type the commands below to install Conda. Follow the instructions for the installation there.
  cd ~/Downloads
  sh Miniconda3-latest-Linux-x86_64.sh
  1. Inside MobaXterm, Follow the instructions on screen replying yes when necessary. Restart your terminal window to apply modifications. After restarting, you can type the command below to install Mamba:
  conda init
  conda install -n base -c conda-forge mamba
  1. Inside MobaXterm, 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. Close and open all application and Inside MobaXterm, you will probably will see that your WSL is already listed on the left panel as an available connection. Just double-click it and you will be accessing it via MobaXterm.

 

On VirtualBox

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

10.  Follow the instructions on screen replying yes when necessary. Restart your terminal window to apply modifications. After restarting, you can type the command below to install Mamba:

  conda init
  conda install -n base -c conda-forge mamba





2. Create a conda environment from file


To download the environment_scRNAseq2022.yml file using the command on Terminal:


curl -o environment_scRNAseq2022.yml https://raw.githubusercontent.com/NBISweden/workshop-scRNAseq/master/labs/environment_scRNAseq2022.yml



After this, you should have a file named environment_scRNAseq2022.yml in your directory (it does not matter where). Next, type:


mamba env create -n scRNAseq2022 -f environment_scRNAseq2022.yml



Several messages will show up on your screen and will tell you about the installation process. This may take a few minutes depending on how many packages are to be installed.


##Collecting package metadata: done
##Solving environment: done
##
##Downloading and Extracting Packages
##libcblas-3.8.0       | 6 KB      | ############################################################################# | 100%
##liblapack-3.8.0      | 6 KB      | ############################################################################# | 100%
##...
##Preparing transaction: done
##Verifying transaction: done
##Executing transaction: done



 


3. Activate the environment


Once the environment is created, we need to activate it in order to use the softwares and packages inside it. To activate an environment type:


conda activate scRNAseq2022



From this point on you can run any of the contents from the workshop. For instance, you can directly launch RStudio by typing rstudio. Here it is important to add the & symbol in the end to be able to use the command line at the same time if needed. You can open other files from Rstudio later as well.


rstudio PATH/my_script.Rmd &



 


4. Deactivate the environment


After you've ran all your analyses, you can deactivate the environment by typing:


conda deactivate