planemo 0.8.0

Command-line utilities to assist in building tools for the Galaxy project (http://galaxyproject.org/).

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

• Free software: Academic Free License version 3.0

• Documentation: https://planemo.readthedocs.org.

• Code: https://github.com/galaxyproject/planemo

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 planemo

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 ~/.planemo.yml) 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 Galaxy releases from 2015.

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.

Experimental Features

Planemo can also be used to explore some more experimental features related to Galaxy tooling - including support for Travis CI, Docker, Homebrew.

Tool Shed

For information on using Planemo to publish artifacts to the Galaxy Tool Shed, check out the Publishing to the Tool Shed documentation on reathedocs.org.

TravisCI

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 integration testing 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 @ http://travis-ci.org/

In this example the file .travis/setup_custom_dependencies.bash should install the dependencies required to test your files on to the Travis user’s PATH.

This testing approach may only make sense for smaller repositories with a handful of tools. For larger repositories, such as tools-devteam or tools-iuc simply linting tool and tool shed artifacts may be more feasible. Check out the .travis.yml file used by the IUC as example.

Docker

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 commands.

Brew

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 - https://github.com/Homebrew/homebrew-science/issues/1191. Information on the implementation can be found https://github.com/jmchilton/platform-brew 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
/home/john/.linuxbrew/Cellar/bowtie2/2.1.0/bin/bowtie2
(bowtie2) % exit
% . <(planemo brew_env bowtie2.xml) # or just source deps in cur env
% which bowtie2
/home/john/.linuxbrew/Cellar/bowtie2/2.1.0/bin/bowtie2

For more information see the documentation for the brew and brew_env commands.

History

0.8.0 (2015-04-27)

• Implement the new shed_lint command that verifies various aspects of tool shed repositories - including XSD validation of repository_dependencies.xml and tool_dependencies.xml files, best practices for README files, and the contents of .shed.yml files. This requires the lxml library to be available to Planemo or the application xmllint to be on its PATH. Pull Request 130 Issue 89 Issue 91 912df02 d26929e 36ac6d8

• Option to enable experimental XSD based validation of tools when lint is executed with the new --xsd flag. This validation occurs against the unofficial Galaxy Tool XSD project maintained by @JeanFred. This requires the lxml library to be available to Planemo or the application xmllint to be on its PATH. Pull Request 130 912df02

• Allow skipping specific linters when using the lint command using the new --skip option. 26e3cdb

• Implement sophisticated options in .shed.yml to map a directory to many, custom Tool Shed repositories during shed operaitons such shed_upload including automatically mapping tools to their own directories and automatically building suites repositories. Pull Request 143

• Make shed_upload more intelligent when building tar files so that package and suite repositories may have README files in source control and they will just be filtered out during upload. 53edd99

• Implement a new shed_init command that will help bootstrap .shed.yml files in the specified directory. cc1a447

• Extend shed_init to automatically build a repository_rependencies.xml file corresponding to a Galaxy workflow (.ga file). Issue 118 988de1d

• In addition to a single file or directory, allow lint to be passed multiple files. 343902d Issue 139

• Add -r/--recursive option to shed_create and lint commands. 63cd431 01f2af9

• Improved output formatting and option to write diffs to a file for the shed_diff command. 965511d

• Fix lint problem when using new Galaxy testing features such as expecting job failures and verifing job output. Issue 138

• Fix typo in test help thanks to first time contributor @pvanheus. Pull Request 129 1982076

• Fix NPE on empty help element when linting tools. Issue 124

• Fix lint warnings when configfiles are defined in a tool. 1a85493

• Fix for empty .shed.yml files. b7d9e96

• Fix the test command for newer versions of nose. 33294d2

• Update help content and documentation to be clear normalize should not be used to update the contents of tool files at this time. 08de8de

• Warn on unknown command attributes when linting tools (anything but interpreter). 4f61025

• Various design, documentation (including new documentation on Tool Shed publishing), and testing related improvements (test coverage has risen from 65% to over 80% during this release cycle).

0.7.0 (2015-04-13)

• Implement shed_create command to create Tool Shed repositories from .shed.yml files (thanks to Eric Rasche). Pull Request 101

• Allow automatic creation of missing repositories during shed_upload with the new --force_repository_creation flag (thanks to Eric Rasche). Pull Request 102

• Allow specifying files to exclude in .shed.yml when creating tar files for shed_upload (thanks to Björn Grüning). Pull Request 99

• Resolve symbolic links when building Tool Shed tar files with shed_upload (thanks to Dave Bouvier). Pull Request 104

• Add a Contributor Code of Conduct. Pull Request 113

• Omit tool_test_output.json from Tool Shed tar file created with shed_upload (thanks to Dave Bouvier). Pull Request 111

• Update required version of bioblend to 0.5.3. Fixed Issue 88.

• Initial work on implementing tests cases for Tool Shed functionality. 182fe57

• Fix incorrect link in HTML test report (thanks to Martin Čech). 4c71299

• Download Galaxy from the new, official Github repository. 7c69bf6

• Update travis_test to install stable planemo from PyPI. 39fedd2

• Enable caching on --install_galaxy by default (disable with --no_cache_galaxy). d755fe7

0.6.0 (2015-03-16)

• Many enhancements to the tool building documentation - descriptions of macros, collections, simple and conditional parameters, etc…

• Fix tool_init to quote file names (thanks to Peter Cock). Pull Request 98.

• Allow ignoring file patterns in .shed.yml (thanks to Björn Grüning). Pull Request 99

• Add --macros flag to tool_init command to generate a macro file as part of tool generation. ec6e30f

• Add linting of tag order for tool XML files. 4823c5e

• Add linting of stdio tags in tool XML files. 8207026

• More tests, much higher test coverage. 0bd4ff0

0.5.0 (2015-02-22)

• Implement --version option. Issue 78

• Implement --no_cleanup option for test and serve commands to persist temp files. 2e41e0a

• Fix bug that left temp files undeleted. Issue 80

• More improvements to release process. fba3874

0.4.2 (2015-02-21)

• Fix setup.py for installing non-Python data from PyPI (required newer for tool_factory command and reStructuredText linting). Thanks to Damion Dooley for the bug report. Issue 83

0.4.1 (2015-02-16)

• Fix README.rst so it renders properly on PyPI.

0.4.0 (2015-02-16)

• Implement tool_init command for bootstrapping creation of new tools (with tutorial.) 78f8274

• Implement normalize command for reorganizing tool XML and macro debugging. e8c1d45

• Implement tool_factory command to spin up Galaxy pre-configured the Tool Factory. 9e746b4

• Added basic linting of command blocks. b8d90ab

• Improved linting of help blocks, including verifying valid reStructuredText. 411a8da

• Fix bug related to serve command not killing Galaxy properly when complete. 53a6766

• Have serve command display tools at the top level instead of in shallow sections. badc25f

• Add additional dependencies to setup.py more functionality works out of the box. 85b9614

• Fix terrible error message related to bioblend being unavailable. Issue 70

• Various smaller documentation and project structure improvements.

0.3.1 (2015-02-15)

• Fixes to get PyPI workflow working properly.

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 bit.ly/gxbrew1 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 https://github.com/galaxyproject/planemo.

• 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