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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
  • annotations module
  • authenticate module
  • configuration module
  • dataset_collections module
  • datasets module
  • datatypes module
  • extended_metadata module
  • folder_contents module
  • folders module
  • forms module
  • genomes module
  • group_roles module
  • group_users module
  • groups module
  • histories module
  • history_contents module
  • item_tags module
  • job_files module
  • jobs module
  • lda_datasets module
  • libraries module
  • library_contents module
  • metrics module
  • page_revisions module
  • pages module
  • provenance module
  • quotas module
  • remote_files module
  • request_types module
  • requests module
  • roles module
  • samples module
  • search module
  • tool_data module
  • tool_dependencies module
  • tool_shed_repositories module
  • tools module
  • toolshed module
  • tours module
  • users module
  • visualizations module
  • webhooks module
  • workflows module