A few weeks ago the god of fried motherboards awarded me the opportunity to buy a new Macbook Pro, and to spend a whole lot of time re-installing software on a clean machine. Although I’m a veteran user of the fink package manager, the first thing I did on this laptop was install the Homebrew package manager which I’ve been fiddling around with as a potentially useful tool for students who need to get UNIX packages working on their computers quickly. To install it, you go to:


At the command line, run the ruby install command given on the homebrew page. Once you’ve done that, it’s easy to install any package you want and make your UNIX more UNIX-y.  There’s also a massive list of software that you can potentially install at the Homebrew Science Tap. If you wanted to install, say, the SRA toolkit, you would type:

brew install sratoolkit

sit back, and wait for your software to be perfectly installed.  Obviously you need to be an admin of your own machine for this to work.  If something’s missing, homebrew will tell me EXACTLY what I need to do to get it done, like in this example where I’m trying to install the maker pipeline but I need some perl modules first:

brew install maker

maker: Unsatisfied dependency: IO::Prompt

Homebrew does not provide Perl dependencies; install with:

cpan -i IO::Prompt

maker: Unsatisfied dependency: IO::All

Homebrew does not provide Perl dependencies; install with:

cpan -i IO::All Error: Unsatisifed requirements failed this build.

sudo cpan -i IO::Prompt

You can literally just cut and paste the cpan install commands to get your dependencies solved in seconds.

Pretty neat, am I right?

We have been using Homebrew to get the computer lab ready for BINF 6215. My life would be much easier if all bioinformatics developers just made their software available as Homebrew packages already.

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