Setup your work environment#
Setup for Mac / Linux users#
You are lucky, using a UNIX based system as always been ideal for bioinformatics.
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/.
Installing Docker#
Installing Docker (specifically Docker Desktop) is quite straightforward on Mac, Windows and Linux distributions. Note that Docker runs as root, which means that you have to have sudo privileges on your computer in order to install or run Docker. When you have finished installing docker, regardless of which OS you are on, please type docker --version to verify that the installation was successful.
Docker for older versions of OSX/Windows
The latest version of Docker may not work if you have an old version of either OSX or Windows. You can find older Docker versions that may be compatible for you if you go to https://docs.docker.com/desktop/ and click "Previous versions" in the left side menu.
MacOS#
Go to mac-install section of the Docker documentation and select the download option that is suitable for your computer’s architecture (i.e. if you have an Intel chip or a Apple silicon chip). This will download a dmg file - click on it when it’s done to start the installation. This will open up a window where you can drag the Docker.app to Applications. Close the window and click the Docker app from the Applications menu. Now it’s basically just to click “next” a couple of times and we should be good to go. You can find the Docker icon in the menu bar in the upper right part of the screen.
Linux#
Go to the linux-install section of the Docker documentation and make sure that your computer meets the system requirements. There you can also find instructions for different Linux distributions in the left sidebar.
Windows#
Go to the windows-install section of the Docker documentation and select the download option that is suitable for your computer’s architecture (i.e. if you have an Intel chip (x86) or ARM). Once the download is complete, execute the file and follow the instructions. You can now start Docker from the Start menu. You can search for it if you cannot find it; the Docker whale icon should appear in the task bar.
You will probably need to enable integration with the Linux subsystem, if you haven’t done so during the installation of Docker Desktop. Right-click on the Docker whale icon in the task bar and select Settings. Choose Resources and select WPS integration. Enable integration with the Linux subsystem and click Apply & Restart; also restart the Linux subsystem.