Workbench-CLI

Irida/Galaxy workbench related tasks automated. Galaxy & Irida server, management cli toolset

Workbench CLI

A getting started DOCUMENTATION for the Workbench okapi
Explore the docs »

Report Bug · Request Feature

Table of Contents

1. About The Project
   • Built With
2. Getting Started
   • Prerequisites
   • Installation
3. Usage
4. Roadmap
5. Contributing
6. License
7. Contact
8. Acknowledgments

About Workbench CLI

![Product Name Screen Shot][product-screenshot]

Workbench-cli is the toolbelt for managing a workbench (consisting of Galaxy and IRIDA) pioneered by SANBI - UWC team.

The workbench has the following high level commands:

• workbench deploy (coming soon)
• workbench install
• workbench start
• workbench stop
• workbench uninstall (coming soon)

Of course, the project will keep developing in fautures and utilities. So I'll be adding more in the near future. You may also suggest changes by forking this repo and creating a pull request or opening an issue. Thanks to all the people have contributed to expanding this Workbench okapi tool!

(back to top)

Built With

This section should list any major frameworks/libraries used to bootstrap your project. Leave any add-ons/plugins for the acknowledgements section. Here are a few examples.

• Python
• Click

(back to top)

Getting Started

This is a cli tool to manage your Workbench (Galaxy and IRIDA) for various microbacterial pathogens.

To get a local copy up and running follow these simple example steps.

Installation

Below is an example of how you can instruct your audience on installing and setting up your app. This template doesn't rely on any external dependencies or services.

Pip Install

  pip install workbench-cli

Configuration

A YAML conf file will be needed to be passed $ workbench-cli launch -c <conf_file location> <service>when launching services on the workbench via the workbench-cli tool.

By default workbench-cli looks at the user home directory for the workbench.yaml file.

The sample for the config file is as follows:

auth:
    basic_auth: True
workbench:
    description: Workbench instance
    fqdn: my.workbench.com
    user: ubuntu
    password: "passw0rd"
    ssh_key: ~/identity.pem
    root_path: /opt/workbench/compose
    irida_api_client_id: "my_client_id"
    irida_api_client_secret: "LKAJHSKJAKJKHAKJSH"
    galaxy_user: "admin@galaxy.org"
    galaxy_api_key: "APIKEY"

(back to top)

Usage

Clone the workbench-deploy repository into the targeted server.:

git clone https://github.com/combat-sars-cov-2/workbench-deploy

1. How to bring the workbench up? $ workbench start
2. How to bring-down the workbench? $ workbench stop
3. How to install GALAXY tools? $ workbench install galaxy-tools
4. How to install IRIDA Plugins? $ workbench install irida-plugins

For more examples, please refer to the Documentation

(back to top)

Contributing

Contributions are what make the open source community such an amazing place to learn, inspire, and create. Any contributions you make are greatly appreciated.

If you have a suggestion that would make this better, please fork the repo and create a pull request. You can also simply open an issue with the tag "enhancement". Don't forget to give the project a star! Thanks again!

1. Fork the Project
2. Create your Feature Branch (git checkout -b feature/AmazingFeature)
3. Commit your Changes (git commit -m 'Add some AmazingFeature')
4. Push to the Branch (git push origin feature/AmazingFeature)
5. Open a Pull Request

(back to top)

License

Distributed under the Apache License. See LICENSE for more information.

(back to top)

Contact

SANBI Team - @combat-sars-cov-2 - info@combat-sars-cov-2.org

Project Link: https://github.com/combat-sars-cov-2/okapi

(back to top)