Create the course conda environment
1. Install Mamba
Follow these instructions to install Conda.
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_spatial2022.yml
file using the command on Terminal:
curl -o environment_spatial2022.yml https://raw.githubusercontent.com/NBISweden/workshop-spatial/main/labs/environment_spatial2022.yml
After this, you should have a file named environment_spatial2022.yml
in your directory (it does not matter where). Next, type:
mamba env create -n spatial2022 -f environment_spatial2022.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 spatial2022
4. Deactivate the environment
After you've ran all your analyses, you can deactivate the environment by typing:
conda deactivate