gratools shell_completion

Introduction

Shell completion is a powerful feature that makes using command-line tools faster and easier. It allows you to auto-complete command names, options, and file paths by pressing the Tab key. The shell_completion command generates the necessary script to enable this for GraTools in your preferred shell (like Bash or Zsh).

Options

Setup Instructions

Follow these three steps to enable shell completion.

Step 1: Generate the Completion Script

Run the command, specifying your shell and a location to save the script. Saving it in your home directory is a simple option.

$ gratools shell_completion --shell bash --output ~

Completion script for bash generated: /home/your_user/gratools-completion.bash
To enable completion, add the following line to your shell configuration file:

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

Step 2: Configure Your Shell

Copy the lines provided in the output and paste them at the end of the appropriate configuration file for your shell. Common files are:

  • Bash: ~/.bashrc

  • Zsh: ~/.zshrc

  • macOS (Bash): You might need to use ~/.bash_profile

Important

You must adapt the path /home/your_user/ to match your own username and the location where you saved the file.

Step 3: Reload Your Shell Configuration

For the changes to take effect, either close and reopen your terminal, or “source” your configuration file directly:

# For Bash
source ~/.bashrc

# For Zsh
source ~/.zshrc

How to Use Shell Completion

Once enabled, you can use the Tab key to complete different parts of a GraTools command.

1. Complete Command Names

Start typing a command and press Tab to see possible completions.

$ gratools list_
list_chr      list_samples

2. Complete Option Names

Type a command followed by – and press Tab to see all available options for that command.

$ gratools get_fasta --

--all-samples             --merge-dist              --output-file-suffix
--chrom-query             --num-threads             --sample-query
--gfa-file-path           --output-directory        --samples-list
--log-path                --start-query             --stop-query
--help                    ...

3. Complete Option Values (e.g., File Paths)

Completion also works for values, like file paths. This is extremely useful for avoiding typos.

# Type this and press Tab
$ gratools stats --gfa-file-path ./data-g

# It will complete to:
$ gratools stats --gfa-file-path ./data-gratools/