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combat-sars-cov-2 / workbench-cli

Workbench-cli is a command-line shell and scripting interface for Galaxy, Irida and other various popular bioinformatics platforms, envisioned to be a Swiss Army knife designed to make life easier for those who love hacking away at the command prompt.
Apache License 2.0
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cli galaxy-project irida

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Workbench-CLI

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


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Workbench CLI

A getting started DOCUMENTATION for the Workbench okapi
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Table of Contents
  1. About The Project
  2. Getting Started
  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:

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!

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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.

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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"

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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

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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

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License

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

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Contact

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

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

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