Introduction to BASH and Sequence Analysis

Author

Hawlader Al-Mamun

Published

July 12, 2024

Installing VS Code and FileZilla

Welcome to the Introduction to BASH class! In this course, we will be exploring the basics of the Bash shell, a powerful tool for interacting with your computer’s operating system. Bash is widely used in bioinformatics for tasks ranging from data processing to system administration. To enhance our learning experience and prepare us for using different bioinformatics software and accessing high-performance computing (HPC) facilities, we will use two key tools: VS Code and FileZilla.

Why Use VS Code and FileZilla?

VS Code (Visual Studio Code):

  • Integrated Terminal: VS Code comes with an integrated terminal that supports Bash, making it a convenient all-in-one tool for writing and executing shell commands.

  • Cross-Platform Compatibility: It works on Windows, macOS, and Linux, ensuring all students can use the same tool regardless of their operating system.

  • Text Editor: VS Code also includes a powerful text editor that supports syntax highlighting and other features that make writing scripts easier and more efficient.

FileZilla:

  • File Transfer Protocol: FileZilla is a free, open-source FTP client that allows you to transfer files between your local machine and a remote server. This is particularly useful for managing files and scripts in a remote environment.

  • Ease of Use: It has an intuitive graphical interface that makes it easy to use, even for beginners.

Installation Instructions

VS Code:

  1. Windows:
  • Download the Visual Studio Code installer for Windows.
  • Once it is downloaded, run the installer (VSCodeUserSetup-{version}.exe). This will only take a minute.
  • By default, VS Code is installed under C:\Users\Username\AppData\Local\Programs\Microsoft VS Code
  1. macOS:
  • Download Visual Studio Code for macOS.
  • Open the browser’s download list and locate the downloaded app or archive.
  • If archive, extract the archive contents. Use double-click for some browsers or select the ‘magnifying glass’ icon with Safari.
  • Drag Visual Studio Code.app to the Applications folder, making it available in the macOS Launchpad.
  • Open VS Code from the Applications folder, by double clicking the icon.
  • Add VS Code to your Dock by right-clicking on the icon, located in the Dock, to bring up the context menu and choosing Options, Keep in Dock.
  1. Linux:
    • Visit the VS Code download page.
    • Follow the instructions specific to your distribution (e.g., Ubuntu, Fedora, etc.).

FileZilla:

  1. Windows:
    • Visit the FileZilla download page.
    • Click on the “Download FileZilla Client” button.
    • Run the installer and follow the prompts to complete the installation.
  2. macOS:
    • Visit the FileZilla download page.
    • Click on the “Download FileZilla Client” button.
    • Open the downloaded file and drag the FileZilla icon to the Applications folder.
  3. Linux:
    • You can install FileZilla via your package manager. For example, on Ubuntu, you can use the command:
     sudo apt-get install filezilla

Preparation for Class

Please ensure you have both VS Code and FileZilla installed on your computer before attending the class. This will allow us to dive straight into the practical aspects of learning Bash without any delays.

We look forward to helping you develop your skills in Bash scripting and system administration. If you encounter any issues during installation, please do not hesitate to reach out for assistance.