Unix 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 installation instructions.

First, create and move into a directory on your computer where it makes sense to work during the course e.g. ~/training-reproducible-research-area.

mkdir ~/training-reproducible-research-area
cd ~/training-reproducible-research-area

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

Open a bash shell Linux terminal and clone the GitHub repository containing all files you will need for completing the tutorials as follows. First, create and move into a directory on your computer where it makes sense to work during the course e.g. ~/training-reproducible-research-area.

mkdir ~/training-reproducible-research-area
cd ~/training-reproducible-research-area

Whenever a setup instruction specifies Mac or Linux (i.e. only those two, with no alternative for Windows), please follow the Linux instructions.

Git#

Chances are that you already have git installed on your computer. You can check by running e.g. git --version in your terminal. 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.

Git configuration will be done together during the training.

Conda#

Conda installation and configuration will be done together during the training event.

Snakemake#

Snakemake installation and configuration will be done together during the training event.

Nextflow#

Nextflow installation and configuration will be done together during the training event.

R Markdown#

R Markdown installation and configuration will be done together during the training event.

Jupyter#

Jupyter installation and configuration will be done together during the training event.

Docker#

Installing Docker is quite straightforward on Mac or Windows and a little more cumbersome on Linux. 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!

macOS intel/M1/M2#

Go to docker.com and select download option that is suitable for your computer's architecture (i.e. if you have an Intel chip or a newer Apple M1 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#

How to install Docker differs a bit depending on your Linux distribution, but the steps are the same. Please follow the instructions for your distribution on https://docs.docker.com/engine/install/#server.

Windows#

In order to run Docker on Windows your computer must support Hardware Virtualization Technology and virtualization must be enabled. This is typically done in BIOS. Setting this is outside the scope of this tutorial, so we'll simply go ahead as if though it's enabled and hope that it works.

On Windows 10 we will install Docker for Windows, which is available at docker.com. Click the link Download from Docker Hub, and select Get Docker. 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.

Singularity#

Singularity installation might be tiedous. No worries if you do not succeed the installation. We can reiew the installation procedure during the training event.

Installation of Singularity depends, again, on your operating system. When you have finished, regardless of your OS, please type singularity --version to verify that your installation was successful!

Both Mac and Windows utilise Vagrant, for which the information in the box below may help you.

Vagrant and VirtualBox
The Vagrant VirtualBox with Singularity can be started like this:

• Move into the folder vm-singularity where you installed Singularity.
• Type vagrant up and once this has finished, verify that the Vagrant VirtualBox is running with vagrant status.
• Now, type vagrant ssh, which will open the Vagrant VirtualBox.
• The first time you open the Vagrant VirtualBox like this, you will have to

macOS intel#

Please follow the Mac-specific instructions at the Singularity website.

macOS M1/M2#

You're out of luck this time, as often with new OS and chip architectures, the tools may not yet be compatible. The proper way here is to use a linux virtual machine. You will have to download a linux distribution iso image and install it via a virtual machine manager. Please follow the instruction here.

Linux#

Follow the Linux-specific instruction at the Singularity website.

Windows#

Please follow the Windows-specific instructions at the Singularity website.