Lessons on HPC for genomics lessons
Adapted from cloud-genomics repository
Where possible, HPC concepts and exercises are merged into the appropriate lesson. This includes:
- variant calling workflow (wrangling-genomics)
Assumptions:
- First round, I will try to be as generic where possible, so that these lessons can work for multiple schedulers. We will, however, include site-specific info (login, filesystems, etc) to be removed later
- Where needed, commands will be specific to SLURM
To-do:
- Abstract materials where it makes sense. This can include using shell variables for places like SCRATCH, TEMP, WORKING_DIR, etc.
- Mark callouts for site-specific information (e.g. login hosts & filesystem names)
- Include similar commands for other schedulers
-Bob Freeman
Original contributors:
- Chris Fields
- [Bob Freeman] (http://twitter.com/devbioinfoguy)
- Adina Howe
- Andréa Matsunaga
- Stephen Turner
- Jason Williams