This repository includes useful tutorials and resources for working in the Capra lab. It can also be found on ACCRE at /dors/capra_lab/resources/.

See an overall Intro to the Capra Lab here.

Tutorials

tutorials made for ourselves

Project directory structure

Tony's rules on how to set up a project directory here

Safe rm on ACCRE

learn how to safely delete files on ACCRE
here

SLURM Scheduling

tips and tricks for scheduling jobs (or: How not to be That Guy)
presented originally by David Rinker and Mike Sivley
presentation

ACCRE virtual environments

How and why to use Conda on ACCRE
presented originally by Mary Lauren Benton, Ling Chen, and Laura Colbran
presentation

Setting up conda environments on DORS
here

Jupyter

Tips and tricks for using Jupyter Notebooks
presented originally by Mary Lauren Benton, Ling Chen, and Laura Colbran
here

Git + Github

Tips and tricks for using Github for version-control
presented originally by Greg Sliwoski
presentation and cheatsheet

Tony's old tutorial here

Good external tutorials:

• Atlassian
• Pro Git

crontabs

how to run jobs automatically
here

Mac set-up

how to set up a Mac for programming and to use ACCRE
here

Advanced Unix: Tips & Tricks

useful commands (sed, awk, grep, etc.) regular expressions, and bash scripting
presented originally by Mary Lauren Benton
here

Good Coding Practices

Tips for keeping your code understandable (comments, functions, argument parsing, etc.)
presented originally by Laura Colbran and Mary Lauren Benton
here

How to keep track of your code

here

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External Resources

resources from around the web

Life Advice

career advice, writing resources, grant text, fun stuff
here

Programming

general resources, Python, R
here

Statistics

basics, specific methods, Machine Learning
here

Genetics

general resources, GWAS, Fst
here

linked_files

contains files linked to by tutorials in this directory