Hosting to UCSC with Custom Builds

usegalaxy.org support
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5

Hi @GalaxyFrog

We discussed this directly but let’s share with the community and the ChatGXY help indexes here too.

Hub genomes - data hosting from a public Galaxy server

These are special and not currently supported for direct data hosting from a public Galaxy server. We have been discussing this for some time! I’ve opened a new issue ticket with all of the details for the use case (hosting bigWig files) but also for visualization purposes. For now, IGV can be used for the visualization with any fasta file (see igv ).

Hub genomes - data hosting workaround in a private Galaxy server

The ticket above also includes the current workaround for custom data hosting into a Hub assembly. In short, you can host a small personal Galaxy instance and connect it to UCSC display. The DOCKER version of Galaxy has most pre-configured, so the start up and data saving parameters are different than a full server from scratch, so please be sure to see the dedicated README.

Workaround for end users

  1. Learn how to host your own Galaxy server here (the Docker version would be recommended for “less” technical user cases!) → Private Galaxy Servers

  2. Learn how to host data in your own Galaxy server into a Hub here → GitHub - goeckslab/hub-archive-creator: This Galaxy tool permits to prepare your files to be ready for Assembly Hub visualization. · GitHub

Fasta preparation

The chromosome lengths will be computed on demand from a fasta file, however, that fasta should be very clean. For your case, this means removing the description content from the fasta title lines.

The NormalizeFasta tool can do this. Please see the extra option to “split title line at first whitespace”. You will want to use this, along with wrapping to a very standard width. Wrapping at 80 bases is the original specification and tends to work best with any tool! If you were working on the command line, both would be needed, and in Galaxy this can be optional, but if you loath odd random errors as much as me, standardizing reference data at the start is a worthwhile time investment.

Not sure how? Please see → FAQ: How to use Custom Reference Genomes?

Thanks for all the follow-up! The developers will review the ticket next Tuesday and we’ll learn about their thoughts back on it directly.