Local IT wiki:
- Servers, printers and other IT issues at the school of earth sciences
- https://itwiki.science.unimelb.edu.au/wiki/Category:Earth_Sciences
Software Carpentry:
- Guides on shell, python, version control and other software development tools for scientists
- http://software-carpentry.org
Shell Course:
- We'll be roughly following this today
- http://software-carpentry.org/v4/shell/index.html
The shell is a text based interface for running programs. It allows for composition of multiple commands, for instance get a list of all files in a directory then do a find/replace on each one, and also allows you to save a list of commands in a script so the same process can be run multiple times, e.g. for multiple input files
The shell is accessed through a program called 'terminal' on your desktop. This is available by default on Linux and OSX, to use the shell commands on Windows you need to install a program called 'Cygwin'
There are multiple different shell types, syntax varies between them. The most used variants are 'bash' and 'tcsh'. Simple commands are mostly identical, loops and conditionals are quite different though. We'll be using 'bash' for this tutorial.
To see your current shell:
$ echo $SHELL
/bin/bash
(lines that start with $ are entered into the command line)
If you're currently using 'tcsh' change to bash:
$ bash