Linux for Biologists
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Linux for Biologists

A Cookbook

About the Book

If you are a student or a researcher in biological sciences and are new to Linux, this book will help you get started quickly.

The primary focus is in using graphical user interfaces (GUIs) to accomplish tasks, but methods using the command line interface are also discussed.

You will learn how to:

  • Run Linux on your computer
  • Use the desktop and included software
  • Work with files and directories
  • Search and install software
  • Run some basic commands
  • Run the Galaxy platform on your computer

Download virtual machine

If you do not have access to a Linux desktop, you can download a virtual machine image from the link below. This will help you run a virtual machine of Linux Mint 20.1 on your computer. All the included recipes has been tested using this distribution.

Download link (SourceForge): linuxmint-20.1.ova

Once downloaded, you can follow the "Running a Linux virtual machine" section in Chapter 2 of the book.

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About the Author

Vimalkumar Velayudhan
Vimalkumar Velayudhan

Hello. I’m Vimal.

I got introduced to Linux and open source software while pursuing my Master’s degree in Biotechnology at Madurai Kamaraj University, India.

The idea of being able to use and modify software without restrictions was new and exciting to me. I learnt to install Linux, compile software from source code and even create my own Linux live CD!

This experience became valuable in academia, where I worked primarily in research support for a period of over 9 years. During this time, I had installed and managed servers, databases and websites, taught beginner level courses in programming and Bioinformatics, contributed in the development of scientific software and published software in repositories.

This book is a compilation of the experiences I had gained over time in my interactions with students, colleagues, and the users of our services.

Thank you for your interest in reading this book. I hope you will find it useful.

Vimalkumar Velayudhan

https://vimalkvn.com

Table of Contents

    • 1. About this book
      • 1.1. Who is it for
        • 1.1.1. What you will learn
      • 1.2. What you will need
        • 1.2.1. Linux desktop
        • 1.2.2. Administrator privileges
      • 1.3. About the author
    • 2. Getting started with Linux
      • 2.1. What is Linux
        • 2.1.1. Linux distribution
        • 2.1.2. Desktop environment
        • 2.1.3. Ways to run a Linux desktop
      • 2.2. Running a Linux virtual machine
        • 2.2.1. Requirements
        • 2.2.2. Importing the virtual machine image
        • 2.2.3. Starting the virtual machine
        • 2.2.4. Stopping the virtual machine
      • 2.3. The desktop
        • 2.3.1. The Cinnamon desktop
        • 2.3.2. Changing system settings
      • 2.4. Available software
        • 2.4.1. Files — manage files and directories
        • 2.4.2. Firefox — browse the web
        • 2.4.3. Text Editor — create and edit text files
        • 2.4.4. LibreOffice — edit documents and spreadsheets
        • 2.4.5. Terminal — access the command-line
        • 2.4.6. Screenshot — take screenshots of desktop or windows
        • 2.4.7. Software Manager — install software from repositories
        • 2.4.8. GNU Image Manipulation Program — edit images
        • 2.4.9. Inkscape — create vector graphics
        • 2.4.10. Notes
      • 2.5. Files and directories
        • 2.5.1. Your home directory
        • 2.5.2. Hidden files and directories
        • 2.5.3. Important files in home directory
        • 2.5.4. File and directory names are case-sensitive
        • 2.5.5. Accessing the root filesystem
        • 2.5.6. Transferring files between systems
    • 3. Getting software on Linux
      • 3.1. The quick and easy method
        • 3.1.1. Requirements
        • 3.1.2. Finding and installing software
        • 3.1.3. Removing installed software
        • 3.1.4. Updating installed software
        • 3.1.5. Notes
      • 3.2. Python packages
        • 3.2.1. Requirements
        • 3.2.2. Searching for a package on PyPI
        • 3.2.3. Installing a Python package
        • 3.2.4. Updating an installed package
        • 3.2.5. Removing an installed package
        • 3.2.6. Using installed packages
        • 3.2.7. Python virtual environments
        • 3.2.8. Notes
      • 3.3. Perl modules
        • 3.3.1. Requirements
        • 3.3.2. Configure local-lib module
        • 3.3.3. Searching for a module on CPAN
        • 3.3.4. Installing a Perl module
        • 3.3.5. Using installed modules
      • 3.4. R packages
        • 3.4.1. Requirements
        • 3.4.2. Starting an R session
        • 3.4.3. Installing an R package from CRAN
        • 3.4.4. Installing an R package from Bioconductor
        • 3.4.5. Updating an R package
        • 3.4.6. Removing an R package
        • 3.4.7. Notes
      • 3.5. Conda packages
        • 3.5.1. Requirements
        • 3.5.2. Installing Conda
        • 3.5.3. Using Conda
        • 3.5.4. Notes
      • 3.6. Debian Packages
        • 3.6.1. Requirements
        • 3.6.2. Installing a Debian Package
        • 3.6.3. Upgrading Installed Software
        • 3.6.4. Removing Installed Software
        • 3.6.5. Notes
    • 4. Using the Linux command line
      • 4.1. Shell and Terminal
        • 4.1.1. The shell prompt
      • 4.2. Commands — an overview
        • 4.2.1. Command options
        • 4.2.2. Getting help on using commands
        • 4.2.3. date — display current date and time
        • 4.2.4. cd — change directory
        • 4.2.5. mkdir — create new directory
        • 4.2.6. rmdir — remove empty directory
        • 4.2.7. ls — list files
        • 4.2.8. cp — copy files
        • 4.2.9. cat — display contents of files or combine them
        • 4.2.10. less — view and navigate file contents
        • 4.2.11. head — print first few lines of a file
        • 4.2.12. tail — print last few lines of a file
        • 4.2.13. mv — move a file or directory
        • 4.2.14. rm — remove files or directories
        • 4.2.15. echo — display text or values of variables
      • 4.3. Other useful commands
        • 4.3.1. df — report disk usage
        • 4.3.2. du — estimate disk usage of files or directories
        • 4.3.3. free — view free and used memory
        • 4.3.4. locate — find files using their names
        • 4.3.5. find — search for files
        • 4.3.6. which — locate a command
      • 4.4. Editing text files using nano
        • 4.4.1. Create new file
        • 4.4.2. Pasting text from clipboard
        • 4.4.3. Saving changes
        • 4.4.4. Exit nano
      • 4.5. Exercise — using the command-line
        • 4.5.1. Summary of steps
        • 4.5.2. Sample data
        • 4.5.3. Install NCBI BLAST+ package
        • 4.5.4. Download query sequence
        • 4.5.5. Download the protein sequence database
        • 4.5.6. Search the database using the query sequence
      • 4.6. Notes
        • 4.6.1. Adding directories to PATH
        • 4.6.2. Dealing with spaces in file names
    • 5. Getting started with Galaxy
      • 5.1. Why use Galaxy?
        • 5.1.1. What can you use Galaxy for?
        • 5.1.2. Why run Galaxy on your computer?
      • 5.2. Running Galaxy on your computer
        • 5.2.1. Check system requirements
        • 5.2.2. Get the latest release of Galaxy
        • 5.2.3. Create a Python virtual environment
        • 5.2.4. Start Galaxy
      • 5.3. Register a user account
        • 5.3.1. Managing your account
      • 5.4. Grant administrator privileges for user
        • 5.4.1. Create a configuration file
        • 5.4.2. Add user to list of admin users
        • 5.4.3. Restart Galaxy
        • 5.4.4. Verify admin access
    • 6. Documentation
      • 6.1. Managing references using Zotero
        • 6.1.1. Installing Zotero
        • 6.1.2. Collecting references from the web
        • 6.1.3. Integrating Zotero in LibreOffice
      • 6.2. Creating a notebook using Zim
        • 6.2.1. Features
        • 6.2.2. Installing Zim
        • 6.2.3. Creating a notebook
        • 6.2.4. Taking notes
        • 6.2.5. Exporting notebook
        • 6.2.6. Enabling plugins
        • 6.2.7. Getting help
    • 7. Glossary
  • Index

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