I’m running my own Galaxy and I want to use it to run the SPAdes assembler as part of a Galaxy pipeline, instead of running SPAdes at my command line with shell scripts. Ostensibly, this should be easy to do by simply installing a SPAdes module in Galaxy from a friendly Tool Shed. Is SPAdes in the Tool Shed? Apparently.
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….
The commands covered here are also (mostly) covered in Chapter 4 of Haddock and Dunn, should you need to review. There are two different ways to navigate around the same set of files on your Mac — via the Finder, pointing and clicking at file and directory icons like you’re probably used to, and at the command line, like a badass. The entire point of this class is to put you on the road to being a badass who doesn’t need their hand held…
The first thing we’re going to do in this class is really simple. To start with, go to your Finder window. Go to the directory Applications: Utilities, find the Grab application, and open it. Use it to capture some screen shots. Make a directory in your Documents folder. Call it something sensible and memorable like “6215-exercises”. Save your screen shots into the 6215-exercises folder.