July / August, 2024

Developed by:
Egon A. Ozer, MD PhD ([email protected])
Ramon Lorenzo Redondo, PhD ([email protected])

For the purposes of this workshop we are using a linux virtual machine to make instruction and troubleshooting more simple. However, as we noted earlier, using a virtual machine is likely not your best long-term option as you start doing more bioinformatics work. In that case you are more than likely going to want to use the full, non-virtualized capacity of your laptop or workstation. Below are some instructions to start getting your computer ready for natively installing and running the software we're using in this workshop.

If you're using a Debian-based Linux system (like Ubuntu, Lubuntu, Mint, others...), then you should more or less be able to follow all the same directions as what we've been doing in this workshop. If you use another distribution type such as RedHat or Fedora, many of the commands will be similar, but software packages are installed using a different packagae distribution system (RPM) and commands (yum). For more information about different linux distributions, see this Wikipedia article.

If you are using Windows or Mac, see below for some extra steps you need to take to start installing and using software.

WSL will allow you to run Linux software natively on a Windows PC. Be aware that WSL requires administrator access to install. Also WSL is command line only access. For more information about installing and using WSL beyond what we are doing here, you can look here.

Make sure that you run PowerShell as an administrator.

Type wsl --install. That's it.

WSL automatically installs Ubuntu Linux, which is a very good choice for bioinformatics and will run very similar to Lubuntu.

In PowerShell, type wsl on the command line. The first time it starts up it may take a few minutes to decompress files and set up. You will also have to set a username and maybe a password.

WSL sets up a separate home folder for Ubuntu. You will want to keep track of where it is in Windows.

1. Open your Windows explorer from the WSL command line: explorer.exe ~ (tilde sign at the end)
2. Drag the folder location into your favorites sidebar in the Windows explorer.

Since, like Linux, MacOS is based on Unix it can use a lot of the same software as Linux, however it's different enough that at least some of the software you're likely to want to use will need to be compiled from source code on the Mac. Much of the compiler software you need to do this does not come automatically installed on the Mac. Instead you need to install the Xcode command line tools to do this.

In the Mac terminal, run the following command:

xcode-select --install

You will get a popup window that asks if you want to install the command line developer tools. Click the "Install" button.

The download and installation will take several minutes. Test the installation after download with the following command:

xcode-select -p

The installation was successful if the output is something like this:

/Library/Developer/CommandLineTools

MacOS does not have a native software package manager like the apt system on Ubuntu to install software packages. The next best thing for the Mac is the software installation service Homebrew. Many of the same packages you install with apt can similarly be installed using Homebrew's brew command.

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

Easy!

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