Duke-GCB/DataC-HPC-genomics

Name: DataC-HPC-genomics

Owner: Duke Center for Genomic and Computational Biology

Description: Lesson on Cloud/HPC for genomics lessons

Forked from: fasrc/DataC-HPC-genomics

Created: 2015-10-05 23:10:40.0

Updated: 2015-09-02 11:31:59.0

Pushed: 2015-09-11 22:18:54.0

Homepage: null

Size: 1756

Language: null

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README

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
• Adina Howe
• Andréa Matsunaga
• Stephen Turner
• Jason Williams