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Command-line utilities to assist in building tools for the Galaxy project (

Project description


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Command-line utilities to assist in building tools for the Galaxy_ project.

* Free software: Academic Free License version 3.0
* Documentation:
* Code:

Quick Start

This quick start demonstrates using ``planemo`` commands to help
develop Galaxy tools. Planemo can quickly be installed via
Homebrew_ or as a more traditional Python project.

To install using Homebrew_ or linuxbrew_:


brew tap galaxyproject/tap
brew install planemo

For a more traditional Python installation simply setup a virtualenv
for ``planemo`` (this example creates a new one in ``.venv``) and then
install with ``pip``.


% virtualenv .venv; . .venv/bin/activate
% pip install git+

Planemo is also available a `virtual appliance
<>`_ for Docker_ or Vagrant_ (bundled
with a preconfigured Galaxy server optimized for tool development).

This quick start will assume you will have a directory with one or more
tool XML files. If none is available, one can be quickly create 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 other tool files or a directory of tool files. ::

% planemo l randomlines.xml

The ``lint`` command takes in a additional options related to
reporting levels, exit code, etc.... These options are descirbed here
or (like all available commands) be accessed by passing it ``--help``.::

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

Once tools are syntically correct - it is time to test. The ``test``
`command <>`_
can be used to test a tool or directory of tools.::

% planemo test --galaxy_root=../galaxy-central randomlines.xml

If no ``--galaxy_root`` is defined, ``planemo`` will check for a default in
<>`_) and finally
search the tool's parent directories for a Galaxy root directory (developing
tools under Galaxy ``tools`` directory is a common development workflow).
Planemo can also download and configure a disposable Galaxy instance just for
testing by passing it ``-install_galaxy`` instead of a Galaxy root.::

% planemo t --install_galaxy

**Warning**: The features of Planemo that require a ``--galaxy_root`` will
only work with the latest ``galaxy-central`` ``default`` branch. Planemo will
not work when used with older versions of Galaxy - even the latest stable
``latest_2014.10.06``. Planemo will stablize with the next release of Galaxy
and serious attempts at backward compatibility going forward will be made at
that time.

Planemo will create a HTML an output report in the current directory named
``tool_test_output.html`` (override with ``--test_output``). `Here <>`_ is 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``.

Finally, when tools are ready to be published to GitHub_, it may be valuable
to setup contineous integration to test changes committed and new pull
requests. `Travis CI <>`_ is a service providing free
testing and deep integration with GitHub_.

The ``travis_init`` `command
will bootstrap a project with files to ease contineous inegration of tools
using a Planemo driven approach inspired by this great `blog post
<>`_ by `Peter Cock <>`_.


% planemo travis_init .
% # setup Ubuntu 12.04 w/tool dependencies
% vim .travis/setup_custom_dependencies.bash
% git add .travis.yml .travis
% git commit -m "Add Travis CI testing infrastructure for tools."
% git push # and register repository @

Experimental Features

While Planemo is very experimental itself - it can also be used to explore
some more experimental features related to Galaxy tooling - including support
for Docker and Brew.


Galaxy has `experimental support
<>`_ for running jobs in
Docker_ containers. Planemo contains tools to assist in development of Docker
images for Galaxy tools.

A shell can be launched to explore the Docker enviornment referenced by tools
that are annotated with publically registered Docker images.::

% $(planemo docker_shell bowtie2.xml)

For Docker containers still in development - a Dockerfile can be associated
with a tool by sticking it in the tool's directory. Planemo can then build
and tag a Docker image for this tool and launch a shell into it using the
following commands.::

% planemo docker_build bowtie2.xml # asssumes Dockerfile in same dir
% $(planemo docker_shell --from_tag bowtie2.xml)

For more details see the documentation for the `docker_build
and `docker_shell


The Galaxy development team is exploring different options for integrating
Homebrew_ and linuxbrew_ with Galaxy. One angle is resolving the tool requirements
using ``brew``. An experimental approach for versioning of brew recipes will be
used. See full discussion on the homebrew-science issues page here - Information on the
implementation can be found until a
more permanent project home is setup.


% planemo brew_init # install linuxbrew (only need if not already installed)
% planemo brew # install dependencies for all tools in directory.
% planemo brew bowtie2.xml # install dependencies for one tool
% which bowtie2
bowtie2 not found
% . <(planemo brew_env --shell bowtie2.xml) # shell w/brew deps resolved
(bowtie2) % which bowtie2
(bowtie2) % exit
% . <(planemo brew_env bowtie2.xml) # or just source deps in cur env
% which bowtie2

For more information see the documentation for the `brew
and `brew_env
<>`_ commands.

.. _Galaxy: (
.. _GitHub:
.. _Docker:
.. _Homebrew:
.. _linuxbrew:
.. _Vagrant:


0.3.0 (2015-02-13)

* Add option (``-r``) to the ``shed_upload`` command to recursively upload
subdirectories (thanks to Eric Rasche). `Pull Request 68`_
* Fix diff formatting in test reports (thanks to Eric Rasche).
`Pull Request 63`_
* Grab updated test database to speed up testing (thanks to approach from
Eric Rasche and Dannon Baker). `Issue 61`_, dff4f33_
* Fix test data command-line argument name (was ``test-data`` now it is
``test_data``). 834bfb2_
* Use ``tool_data_table_conf.xml.sample`` file if
``tool_data_table_conf.xml.test`` is unavailable. Should allow some
new tools to be tested without modifying Galaxy's global
``tool_data_table_conf.xml`` file. ac4f828_

0.2.0 (2015-01-13)

* Improvements to way Planemo loads its own copy of Galaxy modules to prevent
various conflicts when launching Galaxy from Planemo. `Pull Request 56`_
* Allow setting various test output options in ``~/.planemo.yml`` and disabling
JSON output. 21bb463_
* More experimental Brew and Tool Shed options that should not be considered
part of Planemo's stable API. See for more details.
* Fix ``project_init`` for BSD tar (thanks to Nitesh Turaga for the bug
report.) a4110a8_
* Documentation fixes for tool linting command (thanks to Nicola Soranzo).
`Pull Request 51`_

0.1.0 (2014-12-16)

* Moved repository URL to
* Support for publishing to the Tool Shed. `Pull Request 6`_
* Support for producing diffs (``shed_diff``) between local repositories and
the Tool Shed (based on scripts by Peter Cock). `Pull Request 33`_
* Use tool's local test data when available - add option for configuring
``test-data`` target. `Pull Request 1`_
* Support for testing tool features dependent on cached data. 44de95c_
* Support for generating XUnit tool test reports. 82e8b1f_
* Prettier HTML reports for tool tests. 05cc9f4_
* Implement ``share_test`` command for embedding test result links in pull
requests. `Pull Request 40`_
* Fix for properly resolving links during Tool Shed publishing (thanks to Dave
Bouvier). `Pull Request 29`_
* Fix for citation linter (thanks to Michael Crusoe for the bug report). af39061_
* Fix tool scanning for tool files with fewer than 10 lines (thanks to Dan
Blankenberg). a2c13e4_
* Automate more of Travis CI testing so the scripts added to tool repository
can be smaller. 20a8680_
* Documentation fixes for Travis CI (thanks to Peter Cock). `Pull Request 22`_,
`Pull Request 23`_
* Various documentation fixes (thanks to Martin Čech). 36f7cb11_, b9232e55_
* Various smaller fixes for Docker support, tool linting, and documentation.

0.0.1 (2014-10-04)

* Initial work on the project - commands for testing, linting, serving Galaxy
tools - and more experimental features involving Docker and Homebrew. 7d07782_

.. _Pull Request 68:
.. _Issue 61:
.. _Pull Request 63:
.. _Pull Request 56:
.. _Pull Request 51:
.. _Pull Request 40:
.. _Pull Request 29:
.. _Pull Request 22:
.. _Pull Request 23:
.. _Pull Request 33:
.. _Pull Request 6:
.. _Pull Request 1:
.. _ac4f828:
.. _834bfb2:
.. _dff4f33:
.. _a4110a8:
.. _21bb463:
.. _af39061:
.. _20a8680:
.. _44de95c:
.. _82e8b1f:
.. _05cc9f4:
.. _32c6e7f:
.. _7d07782:
.. _a2c13e4:
.. _36f7cb11:
.. _b9232e55:

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