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:
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
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