Below are a list of frequently asked questions (and answers) for users new to Planemo.
What is Planemo?¶
Planemo is a command-line application which is primarily used for developing Galaxy and CWL tools, workflows and training materials. It’s also used for deploying the tools and workflows once developed (tools to the Galaxy ToolShed; workflows to the Intergalactic Workflow Commission) and executing Galaxy-based analyses via the command-line, if you prefer or need to use that rather than Galaxy’s graphical interface.
Is Planemo the right tool for me?¶
- Yes, if you are comfortable using the command-line and one of the following is true:
- You want to use a piece of scientific software not currently available in Galaxy and therefore need to wrap it yourself.
- You want to develop a workflow from individual Galaxy tools and submit it to a community repository such as the Intergalactic Workflow Commission.
- You want to develop CWL tools or workflows.
- You’re writing a tutorial for the Galaxy Training Network and would like to use a pre-prepared template.
- You want to run Galaxy workflows from the command line.
What is the difference between Galaxy and CWL? Which should I use?¶
Galaxy is a web-based scientific analysis platform which provides access to scientific software via a graphical interface. It is also a scientific workflow management system and allows chaining multiple individual tools together to form a complex pipeline, which can be executed as a single tool. If you place a high value on a graphical interface, usability and developing flexible, reusable tools which can easily be adapted for other purposes, Galaxy is the best choice for you.
CWL (Common Workflow Language) is a workflow specification, rather than a workflow management system. It aims to allow the textual description of scientific pipelines in a way that is independent of the particular workflow manager used; if this is important to you, using CWL would be an excellent idea. CWL workflows are supported by a variety of workflow managers, including Toil, cwltool, Arvados and Galaxy.
Both Galaxy and CWL place a high value on community, open-source code and FAIR data analysis.
Can I develop Galaxy tools without Planemo?¶
Yes, you can, but it is more complicated to do so and will take more time. Planemo encourages best practices in software development and follows guidelines agreed on by the Galaxy community, particularly test-driven development.
Where can I learn to write tools?¶
We have a tutorial in this documentation and another incorporated into the Galaxy Training Network, which should get you off to a good start.
If you use the Visual Studio Code editor, we recommend using Planemo in conjunction with the Galaxy Language Server, which encourages development best practices and should greatly improve the speed at which you can develop new Galaxy tools.
How do I set up deployment to the ToolShed with Planemo?¶
We recommend using continuous integration (e.g. GitHub Actions) to achieve this and provide a template repository which you can use to set up a GitHub repository which automatically deploys tools to the ToolShed when a pull request is merged.
If you don’t want to handle tool deployment yourself, you can also submit your tool wrappers to a community repository such as the one provided by the IUC. This also has the advantage that your wrappers will be reviewed by experienced Galaxy users and developers.
How can I automate workflow execution with Planemo?¶
Have a look at this section of the documentation, or this training provided by the Galaxy Training Network.