Command-line utilities to assist in building tools for the Galaxy project (http://galaxyproject.org/).
Project description
Command-line utilities to assist in building and publishing Galaxy tools.
Free software: Academic Free License version 3.0
Documentation: https://planemo.readthedocs.org.
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
0.9.0 (2015-05-03)
Add new logo to the README thanks to @petrkadlec from puradesign.cz and @carlfeberhard from the Galaxy Project. Issue 108
Implement smarter shed_diff command - it now produces a meaningful exit codes and doesn’t report differences if these correspond to attributes that will be automatically populated by the Tool Shed. Issue 167
Use new smarter shed_diff code to implement a new --check_diff option for shed_upload - to check for meaningful differences before updating repositories. Issue 168
Record git commit hash during shed_upload if the .shed.yml is located in a git repository. Issue 170
Allow shed_ operations to operate on git URLs directly. Issue 169
Fail if missing file inclusion statements encountered during .shed.yml repository resolution - bug reported by @peterjc. Issue 158
Improved exception handling for tool shed operations including new --fail_fast command-line option. * Issue 114, Pull Request 173
Implement more validation when using the shed_init command. 1cd0e2d
Add -r/--recursive option to shed_download and shed_diff commands and allow these commands to work with .shed.yml files defining multipe repositories. 40a1f57
Add --port option to the serve and tool_factory commands. 15804be
Fix problem introduced with setup.py during the 0.9.0 development cycle - thanks to @peterjc. Pull Request 171
Fix clone bug introduced during 0.9.0 development cycle - thanks to @bgruening. Pull Request 175
0.8.4 (2015-04-30)
Fix for Travis CI testing picking up invalid tests (reported by @takadonet). Issue 161
Fix tar ordering for consistency (always sort by name) - thanks to @peterjc. Pull Request 164, Issue 159
Fix exception handling related to tool shed operations - thanks to @peterjc. Pull Request 155, b86fe1f
0.8.3 (2015-04-29)
0.8.2 (2015-04-29)
Fix bug with config_init command thanks to @bgruening. Pull Request 151
Fix unnessecary lint warning about parallelism tag reported by @peterjc. 9bf1eab
0.8.1 (2015-04-28)
Fixes for the source distribution to allow installation of 0.8.0 via Homebrew.
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
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
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)
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
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