This contains the Galaxy tool definitions and workflow definitions needed to install the [Core Phylogenomis Pipeline][] into Galaxy. This repository contains two main sections. A set of tools under `tools/` and a workflow implementing the core phylogenomics pipeline under `workflows/`. These can be packaged up and uploaded into a [Galaxy Tool Shed][] and then later installed to an instance of Galaxy. Instructions on how to install your own local Galaxy Tool Shed and Galaxy can be found at [IRIDA Galaxy Setup][].
One small point when setting up Galaxy is that for the pipeline to work properly the default **SQLite** database cannot be used. Instructions on setting up a better database for Galaxy can be found at the [Production Server Setup][] documentation.
