nn Galaxy Resources You Should Know About - 2019 Edition
Resources that will help you use Galaxy in your research
By Dave Clements, ...
Galaxy is a platform, and a community, and a sprawling ecosystem of related projects, efforts, and resources. And, it's hard to keep track of all of it.
This blog post does not keep track of it all either, but it does highlight some resources that we think everyone in the Galaxy should know about it.
This library of training materials has something for everyone. You can learn how to use Galaxy, how to deploy Galaxy, and even how to create new training materials. The library features slides and hands on tutorials that often include complete workflows. If you want to learn about Galaxy then start here
Step by step guides to Galaxy, directly using the Galaxy interface.
You will need compute.
You can describe semantic relationships between your datasets using collections. Running an experiment with 4 replicates, covering 3 conditions over 4 developmental stages? Define your collection once and that have results be logically bundled together in subsequent datasets. Collections are one of several resources you use to support large experimental designs in Galaxy.
Tags enable you to follow data through long and complex analyses. Tags make it easy to tell which datasets in the middle and end of your analyses are derived from which of your input datasets. But you gotta assign them before you start working.
Again, but different.
Do you want the provenance, accessiblility, sharability, reproducibility and visualization that Galaxy offeres? But, you want to access it programmatically? The BioBlend applications programming interface (API) provides access to Galaxy for running analyses from inside your python programs. You can get all the power of Galaxy without any of the clicking. Galaxy is also accessible using the Blend4PHP API.
This is what we do. Supporting each other is the very heart of the Galaxy community.
Have a question or an answer to a question? help.galaxyproject.org is an online support forum for the Galaxy Community. You can ask questions, answer questions, upvote posts, and otherwise tap and expand the knowledge of the community.
The Galaxy community uses Gitter for online chat. Galaxy's Gitter channel is a great place for short questions, and for announcing events/news and for posting kudos to community members. Anyone can read the channel, but you will need a GitHub, Twitter, or GitLab account to post.
Looking for workshops, presentations, training, and meetings about Galaxy? The Galaxy Event Horizon lists every upcoming Galaxy-related event that the the community is aware of. Events happen around the world, in person and on-line, and almost every week of the year. Take a look.
The largest event in the Galactic Year is the Galaxy Community Conference, or GCC. GCCs include training, talks, posters, birds-of-a-feather gatherings, and a CollaborationFest. GCCs are a week-long event bringing together the full breadth and depth of the Galaxy community to share best practices and challenges, experiences and outlooks. GCCs alternate between North America in even years, and not North America in odd years.
It's all about community. There are many Galaxy communities and one (or more) of them may be close to you in space or research interests.
Admin documentation is everywhere. Add some links.
Running your own single-user Galaxy instance on your laptop is easy to do. Administering a multi-user, production-grade Galaxy instance is harder and requires significantly more compute knowledge. In either case, there is training available to help you along the way.
- Go at your own pace admin training is available from the Galaxy Training Network
- In person multi-day admin training is also available, at least twice a year.
- The annual Galaxy Community Conferences offer a dedicated admin training day, followed by a selection of other admin training topics on a second training day.
- Week-long Galaxy Admin training workshops have been offered every year since 2016. The most recent one was in January 2019. The next one will likely be between October 2019 and March 2020 - probably in Europe.
Put your infrastructure under version control.
Really. If you are deploying your own Galaxy service then take a good look at using Ansible, and then start using it. (But beware (!) the imposter (!) Ansible Galaxy (it's actually great too, but it's not us).)
The Galaxy Platform Directory lists over 150 platforms where you can use Galaxy, most of them right now, and most of them for free. This includes public servers, available on the web, right now; academic cloud services; commercial cloud services; and containers and virtual machines you can use right now.
A couple of platform types are worth special mention:
UseGalaxy servers implement a common core set of tools and reference genomes, and are open to anyone to use. They also contain tools and genomes that are local to each server. Each is backed by significant computational resources and they are excellent places to get started with Galaxy, and to share and publish your results. And they are free to use, by anyone.
Several academic cloud services have ready to run Galaxy instances. Many of these are restricted to users within a particular geographic domain, for example, a country, province, or consortium of countries. These are often free to eligible researchers.
Also see CloudLaunch
Searching for anything Galaxy related using web search engines is a frustrating process. You are likely to end up with results about football, cars, chocolate, phones, or, the nemesis of all Galaxy web searches: astronomy. Don't give up! Use the PanGalactic Search box at the top of this and every Galaxy Community Hub page. PGS uses Google Custom search to search only the ~40 or so (yes 40) web sites that are relevant to the one true Galaxy.
Want to know how Galaxy is being used, extended and deployed? The Galaxy Publication library lists over 8000 publications that do just that. Publications are tagged to indicate how each pub relates to Galaxy. If you want to focus in on pubs that focus on or use Galaxy extensively, then take a look at the Galactic and Stellar pubs.
Want to know how to cite Galaxy? See the Citing Galaxy page.
The Galaxy-Announce mailing list is a low-volume, moderated mailing list that recieves monthly emails, highlighting what's happing in the Galaxy Community, and the occassional event-related email. Subscribve to Galaxy-Announce if you want Galactic news delivered to your inbox once a month.
The Galaxy News page is another source of Galactic news. News items get posted here more frequently.
The Galaxy Community is active on Twitter, and Twitter is an excellent way to keep your finger on the pulse of what's going on right now. Here's what to look for:
- #UseGalaxy: The preferred hashtag of the Galaxy community. If you want to find stuff, search for this. (In Japan? Look for #UseGalaxyJP)
- @GalaxyProject, @GalaxyAustralia, @GalaxyUKFriends and @Galaxy_Arabic: These twitter accounts servethe global, Australia, UK and, Arabic speaking Galaxy communities.
The Galactic Blog brings together longer form posts about Galaxy, from all over the web. Want to know more about cloud bursting, CVMFS, or Galaxy R Markdown Tools? You can find posts on these and many other topics in the Galactic Blog