Commonly used phylogenetic methods, Monash HPC access and basic bioinformatics

Tips and Tricks for Computational Work

...or, stuff I wish someone had told me over the years from the very beginning.

Adding to PATH (Mac OS)

Adding an executable to your PATH allows you to run that executable from any directory, instead of having to cd into the directory where the executable lives all the time. In this example, we'll create a simple bash script which just prints "hello world". We'll also create a folder on the desktop which we'll store all our executables in called bin, and add this bin folder to the path.

  1. Create a new folder called bin on your desktop. Within that folder, create an executable named hello: touch hello

  2. Use nano hello to modify the contents of the new file hello, adding: echo "Hello world!" Ctrl-O to save the file, and Ctrl-X to exit.

  3. Change access permissions for the executable. This is just a technical step. chmod +x hello

  4. Modify your PATH file: sudo nano /etc/paths

You should see something like: /usr/local/bin /usr/bin /bin /usr/sbin /sbin These are existing paths, which application installers will add executables to. Add a new line: ~/Desktop/bin

Again, Ctrl-O, Ctrl-X to save and close, then close the terminal with exit to activate the changes.

  1. Start a new terminal, and enter hello to test your executable. You should see Hello world! being printed out.