The following script sets up up a virtual environment called snakemake_tutorial in your scratch area and installs snakemake and it’s dependencies. As several dependency packages are downloaded to run snakemake, Mamba is downloaded first and used to parallelise the process. All packages and and env info is stored in you scratch directory rather than home to avoid hitting the strict file number limits in the home directory.

Next we need to set up the directory tree for this project. Keep this seprate from the snakemake env directory. The following code sets up a directory tree that follows the . Save this code to a file called repo_setup.sh, then run ./repo_setup /scratch/$whoami/snakemake-tutorial.

Move on to run basic snakemake process, or back to snakemake introduction.