Summary and Setup
Before joining HPC Workflow Management with Snakemake, participants should be able to
- login to an HPC system and navigate a UNIX shell.
- edit text files with an editor available on the HPC system.
- submit jobs to a job scheduler present on the HPC system.
It will also be helpful if participants have a basic understanding of writing rules for build automation with Make
This lesson is built with The Carpentries Workbench.
Software Setup
Shell
Snakemake is a command-line tool run on in a so-called shell. Please check the installation instructions to ensure you have the corresponding software installed.
Python
Snakemake is a Python program. Please check the installation instructions to ensure you have a working Python environment.
Snakemake
Please install the snakemake software following [the snakemake installation instructions].
If you are using an high-performance computing (HPC) system, there might be a version of snakemake preinstalled. It can also be installed via spack.io or EasyBuild. Please verify that the version installed is version 8 or newer.