smartgamer / datac-hpc-genomics

Lesson on Cloud/HPC for genomics lessons

cloud-genomics

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