1. Introduction to SeqWare
  2. Installation
  3. Getting Started
  4. SeqWare Pipeline
  5. SeqWare MetaDB
  6. SeqWare Portal
  7. SeqWare Web Service
  8. SeqWare Query Engine
  9. Glossary
  10. Frequently Asked Questions
  11. APIs
  12. Source Code
  13. Plugins
  14. Modules
  15. Advanced Topics
    1. Download the tab-completion script.
    2. Install the script.

Seqware command tab-completion

This document will describe how to achieve tab-completion functionality for SeqWare.

Download the tab-completion script.

Download the script from https://github.com/SeqWare/seqware/releases/download/1.1.0/seqware_bash_completion

From the command line, you can do it like this:

$ wget https://github.com/SeqWare/seqware/releases/download/1.1.0/seqware_bash_completion

Install the script.

The script contains bash code that will tell your system how to perform tab-completion for the seqware command. You will need to execute this script to register this code with your system. To do this, you must ensure that the file is executable.

$ chmod u+x seqware_bash_completion

The script needs to be installed in /etc/bash_completion.d/. If you don’t have access to this directory, you could try installing it to ~/.bash_completion.d/ instead.

$ sudo mv seqware_bash_completion /etc/bash_completion.d/

The script then needs to be executed.

$ /etc/bash_completion.d/seqware_bash_completion

You should now be able to type seqware-<TAB> and see a list of available sub-commands (the changes might not be noticable until you open a new terminal or start a new session):

$ seqware 
annotate      checkdb       create        files         workflow      
bundle        copy          dev           query         workflow-run

This will work on subcommands as well!

$ seqware annotate 
experiment    ius           processing    study         workflow-run  
file          lane          sample        workflow