beginner

Learn Linux basics for Bioinformatics

The command line for people who work on a shared server. Adapted from Linux Journey for an introductory Master's level bioinformatics course.

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Getting Started

Getting Started

What Linux actually is, then reaching your server with ssh, keys and VS Code.

Command Line

The fundamentals: navigating files and directories, and editing them with nano.

Text Manipulation

Text Manipulation

Redirection, pipes, and the tools for slicing text: grep, sort, uniq, cut, sed, awk.

Permissions

Read, write and execute, and how to change them.

Scripting

Variables, conditionals, loops, running many jobs, and how R and Python fit in.

Jobs and Processes

Jobs and Processes

Background jobs, screen sessions that survive a dropped connection, and htop.

Moving Data

Getting files on and off the server: wget, scp, rsync and tar.

Your Environment

Your Environment

Environment variables, PATH, startup files, installing software with conda, and disk space.

Going Further

Users and Groups

Users and Groups

Accounts, groups, root and sudo, and the files behind them.

Packages

Package managers, repositories, and building from source.

Advanced ssh

Config files, agents, jump hosts and port forwarding, once the basics chafe.

Process Utilization

Process Utilization

Monitoring CPU, memory and I/O, and scheduling work with cron.

Logging

Where the system writes things down, and how to read it.

Under the Hood

Linux Distributions

Linux Distributions

Where Linux came from, and how Ubuntu, Debian, Red Hat and the rest differ.

The Filesystem

Disks, partitions, mounting, inodes and symlinks.

Devices

How Linux represents the hardware attached to your machine.

Boot the System

Boot the System

What happens between power on and a login prompt.

Kernel

The core of the operating system, modules and system calls.

Init

How services get started, from SysV through to systemd.

Networking

Network Fundamentals

Network Fundamentals

The models and layers that networking is built on.

Subnetting

IPv4, subnet math, CIDR, NAT and IPv6.

Routing

Routers, routing tables and the protocols between them.

Network Configuration

Network Configuration

Interfaces, routes, DHCP and ARP.

Network Troubleshooting

Network Troubleshooting

ping, traceroute, netstat and packet analysis.

DNS

Everything and more that you wanted to know about DNS.