gratools shell_completion

Boost your productivity with Tab-completion for GraTools commands and options.

⚡ Why use Shell Completion?

Shell completion allows you to auto-complete command names, options, and even file paths by simply pressing the Tab key. It prevents typos, saves time, and helps you discover available options without constantly checking the help menu.

Options

🛠️ View Command Line Options

$ gratools shell_completion
Welcome to GraTools version: '1.1.0.dev7'
@author: GraTools team's
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        \..C../      \.............../            \...TATA.../
 
Please cite our gitlab: https://forge.ird.fr/diade/gratools.git\

Usage: gratools shell_completion [OPTIONS]

  Generates shell completion scripts for GraTools. This enables autocompletion
  for commands, options, and arguments in your terminal, making it easier and
  faster to use the GraTools CLI.
  
  Supported shells: Bash, Zsh, Fish.
  
  After generating the script, you'll need to source it or place it in the
  appropriate directory for your shell to activate autocompletion. Instructions
  will be provided upon script generation.
  
  For more details, see the full documentation:
  https://gratools.readthedocs.io/en/latest/commands/shell_completion.html

Options:
  --shell [bash|zsh|fish]
     Specify your shell type (bash, zsh, or fish) to generate the appropriate
     completion script.  [required]

  --output-file PATH
     Specify the full path (including filename) to save the generated completion
     script. If not provided, defaults to 'gratools-completion.<shell>' in the
     current directory.

  -h, --help
     Show this message and exit.

🚀 Setup Instructions

Follow these three steps to enable completion in your terminal environment.

1️⃣ Generate

Create the script for your specific shell (Bash or Zsh).

2️⃣ Configure

Tell your shell to load this script every time it starts.

3️⃣ Reload

Apply the changes to your current session.

Step 1: Generate the Script

Run the command and specify your shell. We recommend saving it in your home directory.

$ gratools shell_completion --shell bash --output ~

# This creates: ~/gratools-completion.bash

Step 2: Configure your Shell

Add the loading logic to your shell configuration file. Choose your shell below:

🐧 Bash

Append these lines to your ~/.bashrc (or ~/.bash_profile on macOS):

# Add completion for gratools
if [ -f "$HOME/gratools-completion.bash" ]; then
    . "$HOME/gratools-completion.bash"
fi

🐚 Zsh

Append these lines to your ~/.zshrc:

# Add completion for gratools
if [ -f "$HOME/gratools-completion.zsh" ]; then
    source "$HOME/gratools-completion.zsh"
fi

⚠️ Important

Ensure the path in the script matches the actual location where you saved the file in Step 1.

Step 3: Reload Configuration

Apply the changes immediately by “sourcing” your config file:

🐧 Bash

source ~/.bashrc

🐚 Zsh

source ~/.zshrc

🎮 How to Use it

Once configured, try these “magic” Tab sequences:

Type gratools list_ + Tab

⌨️ Commands

$ gratools list_
list_chr      list_samples

Type -- + Tab

🛠️ Options

$ gratools get_fasta --
--all-samples   --num-threads
--chrom-query   --sample-query

Type a path + Tab

📁 Values

$ gratools stats --gfa ./data-g
# Completes to:
$ gratools stats --gfa ./data-gratools/

💡 Pro Tip

If you are using Zsh with a framework like Oh My Zsh, make sure compinit is initialized in your .zshrc before sourcing the GraTools completion script for the best experience.

📑 Quick Links

• Back to Hub: GraTools: A Pangenome GFA Toolkit

• Workflow Guide: 🚀 Quick Start Guide