cli-fundamentals

A repo for sharing-session on efficient ways of using command line application (CLI). This session is mostly aimed for biologists studying phylogenetics and general bioinformatics. It also provides useful command line skills to those who are interested in learning programming languages beyond R.

Requirements:

Computer running Unix-Like operating system: MacOS or Windows Subsystem for Linux.

Schedules

Meeting 1 : CLI Fundamentals

Date: Sunday, 26 Sept 2021

Time: 21:30 CDT (GMT -5)

1. Basic SHELL
2. Bash vs Zsh vs Fish
3. Commonly used commands
4. Using alias

Meeting 2: Working with Text

Date: TBD

1. Text editor
2. Nano vs Vim
3. Basic shell scripting

Meeting 3: Installing CLI Apps

Date: TBD

1. Installing from OS repositories
2. Installing single-executable app
3. Installing python based applications
4. Installing Java based applications
5. Using Bash to simplify Java-based application commands

Meeting 4: Compiling Code

Date: TBD

1. Compiler basic
2. Compiling C/C++ applications
3. Compiling program written in other programming languages, such Rust and Go

Meeting 5: Into Git and GitHub

Date: TBD

1. Intro Git
2. What's the difference between Git and GitHub
3. Setting up our first github repository
4. Working with local Git repository
5. Commonly used Git commands