Galaxy Code Documentation¶
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research.
- Accessible: Users without programming experience can easily specify parameters and run tools and workflows.
- Reproducible: Galaxy captures information so that any user can repeat and understand a complete computational analysis.
- Transparent: Users share and publish analyses via the web and create Pages, interactive, web-based documents that describe a complete analysis.
Two copies of the Galaxy code doumentation are published by the Galaxy Project
- Galaxy-Dist: This describes the code in the most recent official release of Galaxy.
- Galaxy-Central: Describes the current code in the development branch of Galaxy. This is the latest checkin, bleeding edge version of the code. The documentation should never be more than an hour behind the code.
Both copies are hosted at ReadTheDocs, a publicly supported web site for hosting project documentation.
If you have your own copy of the Galaxy source code, you can also generate your own version of this documentation:
$ cd doc
$ make html
The generated documentation will be in doc/build/html/ and can be viewed with a web browser. Note that you will need to install Sphinx and a fair number of module dependencies before this will produce output.
For more on the Galaxy Project, please visit the project home page.
Contents¶
- API Documentation
- Background
- Quickstart
- API Design Guidelines
- API Controllers
annotationsModuleauthenticateModuleconfigurationModuledataset_collectionsModuledatasetsModuledatatypesModuleextended_metadataModulefolder_contentsModulefoldersModuleformsModuleftp_filesModulegenomesModulegroup_rolesModulegroup_usersModulegroupsModulehistoriesModulehistory_contentsModuleitem_tagsModulejob_filesModulejobsModulelda_datasetsModulelibrariesModulelibrary_contentsModulemetricsModulepage_revisionsModulepagesModuleprovenanceModulequotasModulerequest_typesModulerequestsModulerolesModulesamplesModulesearchModuletool_dataModuletool_shed_repositoriesModuletoolsModuleusersModulevisualizationsModuleworkflowsModule
- Application Documentation
- fpconst Module
- galaxy Package
galaxyPackageappModuleconfigModule- Subpackages
- actions Package
- datatypes Package
- eggs Package
- exceptions Package
- external_services Package
- forms Package
- jobs Package
- model Package
- managers Package
- objectstore Package
- openid Package
- quota Package
- sample_tracking Package
- security Package
- tags Package
- tool_shed Package
- tools Package
- util Package
utilPackagealiaspicklerModulebunchModuledebuggingModuleexpressionsModulehash_utilModuleheartbeatModuleinflectionModulejsonModulelrucacheModulememdumpModulenone_likeModuleodictModulesanitize_htmlModuleshed_utilModuleshed_util_commonModulestreamballModuletemplateModuletopsortModule- Subpackages
- visualization Package
- web Package
- webapps Package
- workflow Package
- galaxy_utils Package
- log_tempfile Module
- mimeparse Module
- pkg_resources Module
- psyco_full Module
- Releases
- May 2015 Galaxy Release (v 15.05)
- March 2015 Galaxy Release (v 15.03)
- January 2015 Galaxy Release (v 15.01)
- October 2014 Galaxy Release (v 14.10)
- August 2014 Galaxy Release (v 14.08)
- June 2014 Galaxy Release (v 14.06)
- April 2014 Galaxy Release (v 14.04)
- February 2014 Galaxy Release (v 14.02)
- November 2013 Galaxy Release (v 13.11)
- August 2013 Galaxy Release (v 13.08)
- June 2013 Galaxy Release (v 13.06)
- April 2013 Galaxy Release (v 13.04)
- February 2013 Galaxy Release (v 13.02)
- January 2013 Galaxy Release (v 13.01)
- Galaxy Releases older than v 13.01