https://github.com/galaxyproject/planemo
Command-line utilities to assist in developing Galaxy and Common Workflow Language artifacts - including tools, workflows, and training materials.
https://github.com/galaxyproject/planemo
cli click commonwl hacktoberfest sdk usegalaxy
Last synced: 5 months ago
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Command-line utilities to assist in developing Galaxy and Common Workflow Language artifacts - including tools, workflows, and training materials.
- Host: GitHub
- URL: https://github.com/galaxyproject/planemo
- Owner: galaxyproject
- License: mit
- Created: 2014-10-04T00:21:23.000Z (over 11 years ago)
- Default Branch: master
- Last Pushed: 2025-05-05T11:41:19.000Z (about 1 year ago)
- Last Synced: 2025-05-05T12:43:18.694Z (about 1 year ago)
- Topics: cli, click, commonwl, hacktoberfest, sdk, usegalaxy
- Language: Python
- Homepage: https://planemo.readthedocs.io
- Size: 10.3 MB
- Stars: 93
- Watchers: 21
- Forks: 91
- Open Issues: 300
-
Metadata Files:
- Readme: README.rst
- Changelog: HISTORY.rst
- Contributing: CONTRIBUTING.rst
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.rst
Awesome Lists containing this project
README
.. figure:: https://raw.githubusercontent.com/jmchilton/planemo/master/docs/planemo_logo.png
:alt: Planemo Logo
:align: center
:figwidth: 100%
:target: https://github.com/galaxyproject/planemo
Command-line utilities to assist in developing Galaxy_ and `Common Workflow Language`_ artifacts -
including tools, workflows, and training materials.
.. image:: https://readthedocs.org/projects/planemo/badge/?version=latest
:target: http://planemo.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
.. image:: https://badge.fury.io/py/planemo.svg
:target: https://pypi.python.org/pypi/planemo/
:alt: Planemo on the Python Package Index (PyPI)
.. image:: https://github.com/galaxyproject/planemo/actions/workflows/ci.yaml/badge.svg
:target: https://github.com/galaxyproject/planemo/actions/workflows/ci.yaml?query=branch%3Amaster+event%3Apush
* Free software: MIT License
* Documentation: https://planemo.readthedocs.io.
* Code: https://github.com/galaxyproject/planemo
Quick Start
-----------
-----------------
Obtaining
-----------------
For a traditional Python installation of Planemo, first set up a virtualenv
for ``planemo`` (this example creates a new one in ``.venv``) containing
Python 3.8 or newer and then install with ``pip``. Planemo must be installed
with pip 7.0 or newer.
::
$ python -m venv .venv; . .venv/bin/activate
$ 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_ and
`Common Workflow Language`_ tool development.
You can choose from open virtualization format (OVA_, .ova) or Docker_
appliances.
-----------------
Basics - Galaxy
-----------------
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 ``project_init --template=demo mytools; cd mytools``.
Planemo can check tool XML files 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 download and configure
a disposable Galaxy instance for testing.
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`_.
For more information on developing Galaxy workflows with Planemo checkout
`best practices for Galaxy Workflows`_ and the description of Planemo's
`test format`_. For information on developing Galaxy training materials
checkout the `contributing documentation `__
on training.galaxyproject.org.
----------------------------------
Basics - Common Workflow Language
----------------------------------
This quick start will assume you have a directory with one or more `Common Workflow
Language`_ YAML files. If no such directory is available, one can be quickly created for
demonstrating ``planemo`` as follows ``planemo project_init --template=seqtk_complete_cwl mytools; cd mytools``.
Planemo can check tools YAML files 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 seqtk_seq.cwl
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 CWL tool, workflow, or a directories thereof.
::
$ planemo test --engine cwltool seqtk_seq.cwl
Planemo will create a HTML output report in the current directory named
``tool_test_output.html``. Check out the file ``seqtk_seq_tests.yml`` for
an example of Planemo test for a CWL tool. A test consists of any number of
jobs (with input descriptions) and corresponding output assertions.
Checkout the `Commmon Workflow User Guide`_ for more information on developing
CWL tools in general and `Building Common Workflow Language Tools`_ for more
information on using Planemo to develop CWL tools.
---------
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 the `Galaxy `__ or `CWL
`__ version of the "Dependencies and Conda" tutorial
for more information.
-----------------------
Docker and Containers
-----------------------
Planemo can help develop tools that run in "Best Practice" containers for
scientific workflows. Check out the `Galaxy `__ or `CWL
`__ version of the "Dependencies and Containers" tutorial for more information.
.. _Galaxy: http://galaxyproject.org/
.. _GitHub: https://github.com/
.. _Conda: http://conda.pydata.org/
.. _Docker: https://www.docker.com/
.. _Vagrant: https://www.vagrantup.com/
.. _Travis CI: http://travis-ci.org/
.. _`tools-devteam`: https://github.com/galaxyproject/tools-devteam
.. _`tools-iuc`: https://github.com/galaxyproject/tools-iuc
.. _Building Galaxy Tools Using Planemo: http://planemo.readthedocs.io/en/latest/writing_standalone.html
.. _Publishing to the Tool Shed: http://planemo.readthedocs.org/en/latest/publishing.html
.. _Common Workflow Language: https://www.commonwl.org/
.. _Commmon Workflow User Guide: http://www.commonwl.org/user_guide/
.. _Building Common Workflow Language Tools: http://planemo.readthedocs.io/en/latest/writing_cwl_standalone.html
.. _OVA: https://en.wikipedia.org/wiki/Open_Virtualization_Format
.. _test format: https://planemo.readthedocs.io/en/latest/test_format.html
.. _best practices for Galaxy Workflows: https://planemo.readthedocs.io/en/latest/best_practices_workflows.html