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This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Galaxy API Documentation

In addition to being accessible through a web interface, Galaxy can also be accessed programmatically, through shell scripts and other programs. The web interface is appropriate for things like exploratory analysis, visualization, construction of workflows, and rerunning workflows on new datasets.

The web interface is less suitable for things like

• Connecting a Galaxy instance directly to your sequencer and running workflows whenever data is ready.
• Running a workflow against multiple datasets (which can be done with the web interface, but is tedious).
• When the analysis involves complex control, such as looping and branching.

The Galaxy API addresses these and other situations by exposing Galaxy internals through an additional interface, known as an Application Programming Interface, or API.

Various language specific bindings for interfacing with the Galaxy API have been developed by the Galaxy community including Python, PHP, Java, and JavaScript.

Overview of available API resources is available at https://galaxyproject.org/develop/api/ .

• Quickstart
• Development Guidelines
• Documentation
  • galaxy.webapps.galaxy.api.annotations module
  • galaxy.webapps.galaxy.api.authenticate module
  • galaxy.webapps.galaxy.api.cloud module
  • galaxy.webapps.galaxy.api.cloudauthz module
  • galaxy.webapps.galaxy.api.configuration module
  • galaxy.webapps.galaxy.api.container_resolution module
  • galaxy.webapps.galaxy.api.dataset_collections module
  • galaxy.webapps.galaxy.api.datasets module
  • galaxy.webapps.galaxy.api.datatypes module
  • galaxy.webapps.galaxy.api.display_applications module
  • galaxy.webapps.galaxy.api.dynamic_tools module
  • galaxy.webapps.galaxy.api.extended_metadata module
  • galaxy.webapps.galaxy.api.folder_contents module
  • galaxy.webapps.galaxy.api.folders module
  • galaxy.webapps.galaxy.api.forms module
  • galaxy.webapps.galaxy.api.genomes module
  • galaxy.webapps.galaxy.api.group_roles module
  • galaxy.webapps.galaxy.api.group_users module
  • galaxy.webapps.galaxy.api.groups module
  • galaxy.webapps.galaxy.api.histories module
  • galaxy.webapps.galaxy.api.history_contents module
  • galaxy.webapps.galaxy.api.item_tags module
  • galaxy.webapps.galaxy.api.job_files module
  • galaxy.webapps.galaxy.api.job_ports module
  • galaxy.webapps.galaxy.api.jobs module
  • galaxy.webapps.galaxy.api.libraries module
  • galaxy.webapps.galaxy.api.library_contents module
  • galaxy.webapps.galaxy.api.library_datasets module
  • galaxy.webapps.galaxy.api.metrics module
  • galaxy.webapps.galaxy.api.page_revisions module
  • galaxy.webapps.galaxy.api.pages module
  • galaxy.webapps.galaxy.api.plugins module
  • galaxy.webapps.galaxy.api.provenance module
  • galaxy.webapps.galaxy.api.quotas module
  • galaxy.webapps.galaxy.api.remote_files module
  • galaxy.webapps.galaxy.api.roles module
  • galaxy.webapps.galaxy.api.search module
  • galaxy.webapps.galaxy.api.tags module
  • galaxy.webapps.galaxy.api.tool_data module
  • galaxy.webapps.galaxy.api.tool_dependencies module
  • galaxy.webapps.galaxy.api.tool_entry_points module
  • galaxy.webapps.galaxy.api.tool_shed_repositories module
  • galaxy.webapps.galaxy.api.tools module
  • galaxy.webapps.galaxy.api.toolshed module
  • galaxy.webapps.galaxy.api.tours module
  • galaxy.webapps.galaxy.api.uploads module
  • galaxy.webapps.galaxy.api.users module
  • galaxy.webapps.galaxy.api.visualizations module
  • galaxy.webapps.galaxy.api.webhooks module
  • galaxy.webapps.galaxy.api.workflows module