Prerequisites

Prerequisites

Before attending, you should be comfortable writing some code in python or R, including basics:

• Conditionals/if statements.
• Iteration.
• Reading from files, writing to files.
• Taking arguments on the command line.
• Use of functions.
• Data types.
• Data frames/arrays (R) or numpy arrays (python). Indexing into them.

It would also be helpful if you were familiar with:

• Plotting in ggplot2 or matplotlib.
• Some experience/use of functional programming, such as lapply in R.

Setup

• If you have a Windows computer, please install Ubuntu through WSL
• If you have a Mac, and it has an M1 chip, that you either have access to codon or you have set up conda with intel packages
• Install vscode, and extensions for python.

Session 2

• Make sure you have an account and can submit jobs on codon (at EBI) or a similar HPC environment at your own institution.

Session 3

• Install the rust toolchain, and check you can compile and run the test program.
• Install the rust-analyzer vscode extension. See the guide here https://code.visualstudio.com/docs/languages/rust.
• Check that you can debug a rust test program in vscode.

Session 4

• Set up a github account. You can get a pro account for free with an EBI email.
• Set up ssh key access for your github account.