Do I need to learn Linux?

Maybe not, most likely yes.

Most bioinformatics software are built for Unix-like operating systems. One reason for this is that bioinformatics projects tend to be free and open-source and so need a similar ecosystem. Another reason is that bioinformatics tools need to run on high-performance-computing environments or on cloud computing resources, all of which run on Unix-like systems.

How to install?

Luckily, even if you are only used to Windows, it is very easy these days to install a modern Linux OS on a virtual machine using VirtualBox or VMware or WSL. Here are some guides that might be helpful:

Install Linux via WSL

• https://learn.microsoft.com/en-us/windows/wsl/about

• Enabling GPU passthrough: https://docs.nvidia.com/cuda/wsl-user-guide/

Install Linux on a VM

• https://laptops.eng.uci.edu/engineering-software/using-linux/how-to-set-up-linux-in-a-vm-virtual-machine

• https://ubuntu.com/tutorials/how-to-run-ubuntu-desktop-on-a-virtual-machine-using-virtualbox#1-overview

Install on hardware

• https://ubuntu.com/tutorials/install-ubuntu-desktop#1-overview

Command line

The strength of Unix-like OS is a powerful shell that allows you to write commands for the OS to perform. This especially useful when dealing with huge data files, as is often the case in bioinformatics.

Here are some tutorials that might come in handy in your journey to be a super command-line user.

Basic Bash commands

• https://learn.microsoft.com/en-us/training/modules/bash-introduction/1-what-is-bash

• https://www.digitalocean.com/community/tutorials/linux-commands

Text processing: grep, awk, and sed

• https://www.digitalocean.com/community/tutorials/grep-command-in-linux-unix

• https://www.gnu.org/software/gawk/manual/html_node/Getting-Started.html

• https://rc.fas.harvard.edu/wp-content/uploads/2017/03/AWK.pdf

• https://www.digitalocean.com/community/tutorial-series/using-sed

Displaying text files: cat and less

• https://www.ibm.com/docs/fi/aix/7.2?topic=c-cat-command

• https://linuxhandbook.com/less-command/

Text editors: nano, vim, and emacs

(Choose your editor)

• https://staffwww.fullcoll.edu/sedwards/Nano/IntroToNano.html

• https://web.stanford.edu/class/cs107/resources/vim

• https://www.gnu.org/software/emacs/tour/

Compressing and extracting files: tar, zip, and unzip

• https://www.digitalocean.com/community/tutorials/an-introduction-to-file-compression-tools-on-linux-servers

• https://linux.die.net/man/1/zip

• https://linux.die.net/man/1/unzip

Downloading files: wget and curl

• https://www.digitalocean.com/community/tutorials/how-to-use-wget-to-download-files-and-interact-with-rest-apis

• https://curl.se/docs/tutorial.html

Downloading from and uploading to cloud storage

• Google Drive: wkentaro/gdown

• Zenodo: jhpoelen/zenodo-upload

• Google Drive, Amazon S3, etc.: https://rclone.org/

Managing processes: ps, top, and kill

• https://www.digitalocean.com/community/tutorials/process-management-in-linux

Managing multiple terminals: tmux and screen

• tmux/tmux

• https://www.gnu.org/software/screen/manual/screen.html

Editing the PATH environment variable

• https://www.digitalocean.com/community/tutorials/how-to-view-and-update-the-linux-path-environment-variable