Best Practices for Creating Galaxy Tools#

This page is written by experienced tool developers and contains information about what practices in Galaxy tool development tend to be the most successful ones.

Why you might read this#

If you need to maintain existing tools or develop new tools for Galaxy, this programmer oriented guide, contributed by the community, will detail current collected best practice guidelines for building and maintaining automatically installing reproducible Galaxy tools.

Definitions#

What follows is a short summary of the key parts when it comes to Galaxy Tools.

ToolShed, The Galaxy AppStore - companion Galaxy web server for tools. E.g. https://toolshed.g2.bx.psu.edu or localhost:9009 for Mercurial based source code management and automated installation of all components described below through any Galaxy admin interface.
Galaxy Tool - An application specific, XML defined interface and associated documentation exposing any command line application as a form-driven Galaxy tool - e.g. BWA or bamtools. Ideally, as a shareable tool shed repository, supporting automated Galaxy installation with revision/version specific control of dependency binaries for reproducible analyses.
DataManagers - Large scale scientific analyses often involve local copies of canonical reference data such as reference genomes and application specific index files for annotation and mapping in genomics. In most cases these are rapidly evolving and a constant drain on highly skilled resources to keep up to date manually. Data Managers can be built and shared to automate reference data maintenance by the local Galaxy administrators. Data Manager repositories should start with data_manager_.