Galaxy: introduction

Galaxy is the definitive workflow platform for computational biology. In Galaxy parlance, a workflow is simply a recipe for analyzing data that typically consists of multiple steps, multiple tools, etc. Taking an example from some of our microbiome work, a single workflow could encapsulate quality filtering raw 454 reads stored in FASTA format, computing an alignment, mapping the aligned sequences, and then computing diversity statistics. Sure, creating workflows like the above reduce duplication of effort, but arguably more importantly it enhances reproducibility.

Galaxy really shines with its ability to save and share reproducible workflows. For each workflow, Galaxy saves the exact tool versions used when the workflow was created, and when possible, will always use those specific versions when the workflow is run again. The workflows published by the Galaxy main community are publicly searchable here, but your own workflows can also be shared privately with certain users or exported as a file and saved to your computer.

Galaxy features a web-based graphical user interface that makes powerful analyses possible without doing computer programming. The Galaxy Wikipedia page is a good place to start if you don’t know anything about Galaxy. Galaxy 101 is the first tutorial to follow. There are lots of screencasts out there that show how to use Galaxy, however it’s important to note that only the screencasts on the Galaxy Vimeo channel are up to date. Here’s a good starter:

Learning Resources from Galaxy Project on Vimeo.

They point you to the published pages and in particular the Galaxy exercises, as well as the wiki with its list of learning resources.

Our Galaxy instance is at In addition to some tools we have put together for FHCRC use, we also have imported a number of tools that were of interest to FHCRC scientists. If what you see there doesn’t meet your needs, take a look at the Galaxy toolshed and its documentation. If you find a tool there that we don’t have yet, let Erick know and we’ll work to make it available for you to use.

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