Summary and Schedule
This lesson introduces an approach to combining computing tasks into workflows, which can be used to orchestrate the execution of the individual tasks across nodes in a high-performance computing (HPC) system.
Before joining Building HPC Workflows 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, but this is not an essential requirement.
| Setup Instructions | Download files required for the lesson | |
| Duration: 00h 00m | 1. Running commands with Snakemake | “How do I run a simple command with Snakemake?” |
| Duration: 01h 00m | 2. Running Snakemake on the cluster | “How do I run my Snakemake rule on the cluster?” |
| Duration: 01h 50m | 3. Placeholders | “How do I make a generic rule?” |
| Duration: 03h 00m | 4. MPI applications and Snakemake | “How do I run an MPI application via Snakemake on the cluster?” |
| Duration: 03h 50m | 5. Chaining rules |
“How do I combine rules into a workflow?” “How do I make a rule with multiple inputs and outputs?” |
| Duration: 05h 00m | 6. Processing lists of inputs |
“How do I process multiple files at once?” “How do I combine multiple files together?” |
| Duration: 06h 20m | Finish |
The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.
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.