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Public Galaxy Servers

This repository provides a machine readable list of public Galaxy instances. Instances listed here must be:

  • open to registration
  • available on the public internet
  • generally available (not offline for extended periods of time)

Running the Parser

The European Galaxy team runs the main copy of this code, and we make our results publicly available. If you wish to run a copy of this code, please be considerate of the servers you are probing. We make our requests at most once per hour.

The process.py script contacts every server listed in the file passed to it and collects the results as a .json file an output directory.

$ make servers.csv
$ python process.py servers.csv --json_dir log_directory

If you are running an InfluxDB server, there are a couple of flags to help send data there.

For creating the badges, we provide a second script, badges.py which processes the directory of .json files from the first step and produces a set of .svg files using the API of shields.io

$ python badges.py log_directory output-badges

Data Format

servers.csv is created as a CSV file with a single header line. The columns are:

Column Example Meaning
name Main The name of the server. Often corresponds with the "Galaxy Brand"
url https://usegalaxy.org The URL at which this Galaxy can be accessed. This must be accessible directly, without any redirects or login pages. Otherwise, the Galaxy will be considered as "down" and possibly removed from the list.
support [email protected] A contact address for obtaining support relating to this instance.
location US 2-letter country code where the server/organisation reside.
tags tools The general purpose of this galaxy. E.g. tools for general purpose servers, or nlp for instances focused on natural language processing.

Help us!

This list is never complete. Please feel free to add your own server if your instance meets the requirements.

Scripts

We've included a tool-counting script, tool-count.py. Usage:

$ curl https://usegalaxy.org/api/tools | python tool-count.py usegalaxy.org
galaxy.tools,server=usegalaxy.org count=935,uniq=922

License

The scripts are available under the MIT license. The servers.csv file is released to the public domain, under CC0 1.0.