Command-line utilities to assist in building and publishing Galaxy tools.

• Free software: Academic Free License version 3.0
• Documentation: https://planemo.readthedocs.io.
• Code: https://github.com/galaxyproject/planemo

Quick Start

This quick start demonstrates using planemo commands to help develop Galaxy tools.

Obtaining

For a traditional Python installation of Planemo, first set up a virtualenv for planemo (this example creates a new one in .venv) and then install with pip. Planemo requires pip 7.0 or newer.

$ virtualenv .venv; . .venv/bin/activate
$ pip install "pip>=7" # Upgrade pip if needed.
$ pip install planemo

For information on updating Planemo, installing the latest development release, or installing planemo via bioconda - checkout the installation documentation.

Planemo is also available as a virtual appliance bundled with a preconfigured Galaxy server and set up for Galaxy tool development. You can choose from open virtualization format (OVA, .ova), Docker, or Vagrant appliances.

Basics

This quick start will assume you have a directory with one or more Galaxy tool XML files. If no such directory is available, one can be quickly created for demonstrating planemo as follows mkdir mytools; cd mytools; planemo project_init --template=demo.

Planemo can check tools containing XML for common problems and best practices using the lint command (also aliased as l).

$ planemo lint

Like many planemo commands - by default this will search the current directory and use all tool files it finds. It can be explicitly passed a path to tool files or a directory of tool files.

$ planemo l randomlines.xml

The lint command takes in additional options related to reporting levels, exit code, etc. These options are described in the docs or (like with all commands) can be accessed by passing --help to it.

$ planemo l --help
Usage: planemo lint [OPTIONS] TOOL_PATH

Once tools are syntactically correct - it is time to test. The test command can be used to test a tool or a directory of tools.

$ planemo test --galaxy_root=../galaxy randomlines.xml

If no --galaxy_root is defined, planemo will check for a default in ~/.planemo.yml and finally search the tool's parent directories for a Galaxy root directory. Planemo can also download and configure a disposable Galaxy instance for testing. Pass --install_galaxy instead of --galaxy_root.

$ planemo t --install_galaxy

Planemo will create a HTML output report in the current directory named tool_test_output.html (override with --test_output). See an example of such a report for Tophat.

Once tools have been linted and tested - the tools can be viewed in a Galaxy interface using the serve (s) command.

$ planemo serve

Like test, serve requires a Galaxy root and one can be explicitly specified with --galaxy_root or installed dynamically with --install_galaxy.

For more information on building Galaxy tools in general please check out Building Galaxy Tools Using Planemo.

Tool Shed

Planemo can help you publish tools to the Galaxy Tool Shed. Check out Publishing to the Tool Shed for more information.

Conda

Planemo can help develop tools and Conda packages in unison. Check out Dependencies and Conda for more information.

Docker

Planemo can help develop tools deployable via Docker. Check out Dependencies and Docker for more information.

Common Workflow Language

Planemo includes experimental support for running a subset of valid Common Workflow Language (CWL) tools using either the reference implementation cwltool or a fork of Galaxy enhanced to run CWL tools.

$ planemo project_init --template cwl_draft3_spec
$ planemo serve --cwl cwl_draft3_spec/cat1-tool.cwl

Checko out Building Common Workflow Language Tools for more information.