Summary and Schedule
This is a new lesson built with The Carpentries Workbench.
| 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.
FIXME: Setup instructions live in this document. Please specify the tools and the data sets the Learner needs to have installed.
Data Sets
Download the data zip file and unzip it to your Desktop
Software Setup
Details
Setup for different systems can be presented in dropdown menus via a
solution tag. They will join to this discussion block, so
you can give a general overview of the software used in this lesson here
and fill out the individual operating systems (and potentially add more,
e.g. online setup) in the solutions blocks.
Use PuTTY
Use Terminal.app
Use Terminal