Setup your work environment#
Setup for Mac / Linux users#
You are lucky, using a UNIX based system as always been ideal for bioinformatics.
Open a bash shell terminal and follow the git installation instruction.
Setup for Windows users#
Using a Windows computer for bioinformatic work has sadly not been ideal most of the time, but large advanced in recent years have made this quite feasible through the Windows 10 Linux subsystem. This is the only setup for Windows users that we allow for participants of this course, as all the material has been created and tested to work on Unix-based systems.
Using the Linux subsystem will give you access to a full command-line bash shell based on Linux on your Windows 10 PC. For the difference between the Linux Bash Shell and the PowerShell on Windows 10, see e.g. this article.
Install Bash on Windows 10, follow the instructions at e.g. one of these resources:
- Installing the Windows Subsystem and the Linux Bash
- Installing and using Linux Bash on Windows
- Installing Linux Bash on Windows
Note
If you run into error messages when trying to download files through the Linux shell (e.g. curl:(6) Could not resolve host) then try adding the Google nameserver to the internet configuration by running sudo nano /etc/resolv.conf then add nameserver 8.8.8.8 to the bottom of the file and save it.
Tip
You can find the directory where the Linux distribution is storing all its files by typing explorer.exe .. This will launch the Windows File Explorer showing the current Linux directory. Alternatively, you can find the Windows C drive from within the bash shell Linux terminal by navigating to /mnt/c/.
Open a bash shell Linux terminal and follow the (git installation instruction)[installing-git].
Installing Git#
Chances are that you already have git installed on your computer. You can check by running e.g. git --version. If you don't have git, install it following the instructions here. If you have a very old version of git you might want to update to a later version.