Irida/Galaxy workbench related tasks automated. Galaxy & Irida server, management cli toolset
A getting started DOCUMENTATION for the Workbench okapi
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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!
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.
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.
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
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"
Clone the workbench-deploy repository into the targeted server.:
git clone https://github.com/combat-sars-cov-2/workbench-deploy
- How to bring the workbench up?
$ workbench start
- How to bring-down the workbench?
$ workbench stop
- How to install GALAXY tools?
$ workbench install galaxy-tools
- How to install IRIDA Plugins?
$ workbench install irida-plugins
For more examples, please refer to the Documentation
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!
- Fork the Project
- Create your Feature Branch (
git checkout -b feature/AmazingFeature
) - Commit your Changes (
git commit -m 'Add some AmazingFeature'
) - Push to the Branch (
git push origin feature/AmazingFeature
) - Open a Pull Request
Distributed under the Apache License. See LICENSE
for more information.
SANBI Team - @combat-sars-cov-2 - info@combat-sars-cov-2.org
Project Link: https://github.com/combat-sars-cov-2/okapi