The Shell For Scientists

I’ve posted a half-day “The Shell for Scientists” tutorial that I’ve given variants on a number of times; the motivating problem, provided by Greg Wilson for a two-day set of of tutorials at the University of Toronto, was cleaning up a bunch of auditory lab data on people’s cochlear implants.

The focus is on productivity and automation; PDF slides are available here (although I really should translate them into a markdown-based format to make them more re-usable).

Covered are a number of basic shell commands

• echo
• pwd
• cd
• ls
• man
• file
• cat
• more
• wc
• mv
• cp
• rm
• head
• tail
• sort
• mkdir
• rmdir
• grep
• for..do..done

As well as simple script writing. There is some optional material on make (again, for automation) and ssh/scp (because that was frequently necessary for tutorials at SciNet). There are a number of hands-on exercises sprinkled throughout.