For loops in bash

*Note to all users: As of 07/14/2019, all posts have been moved to (and are being updated at . I don’t have plans to shut this site down, but I have no idea how long it will be maintained by the university in the future.*

A collection of really useful links for bash scripting

For loops:

Here are some links to tutorials I’ve compiled so you can get some extra practice using/crafting for loops. All of these will contain information we haven’t covered yet in addition to the basic for loop.

Warning about using the output of ‘ls’ as a set for a for loop:

More bash goodies:

Test your skills!!

Environment to test out code if you think something weird might be going on with your setup (warning – there might also be something weird with this setup, I haven’t played with it a whole lot).

Regex Practice


Lots of options for practice – choose your favorite!

Regex combined with sed and awk:

Regex golf – match a string with the shortest possible expression:

Bash scripting cheatsheet:
Common/userful bash one-liners:
Friend’s github page with too much awesome information to put it into any other category – spend some time digging around:


Biocomputing Students: hello!

Beginning of the Semester Info

My office is located at Galvin 175. My lab is Galvin 004. My office hours are Thursdays from 5-6PM (recently changed from 4-5). I’ll be in Jordan near the coffee.

My email is

Here’s a friendly link to get you started with installation of UNIX (if you have Windows. Mac users, you don’t need to install anything. Yet.):

(Note: if you have already installed Cygwin/Ubuntu/etc., there are some tips at the bottom so check it out.)

Slides from Week 1 (8/23):