After maintaining the current Galaxy-Apollo instance for over ten years, our hardware cluster is aging out. Rather than upgrading, we are transferring our primary workflows to the main European Galaxy instance and will discontinue our genome annotation services hosted at cpt.tamu.edu.
Our most-used custom tools and workflows are progressively being transferred to Phage Galaxy, hosted by the main European Galaxy instance and accessible at https://phage.usegalaxy.eu. At this large public Galaxy instance anyone can register a free account. We plan to rebuild most of our annotation workflows and a connection to an Apollo annotation system at Phage Galaxy. This Galaxy instance also hosts commonly used tools such as FastQC and SPAdes for genome assembly, among many others. Importantly, their Galaxy instance is maintained by a community much larger than ours at the CPT Galaxy. This migration enables sustainable, long-term open access to quality phage genome annotation tools in one place for our user community.
What about my data?
All users are responsible for downloading and archiving their own data from the CPT system. Once the CPT system goes offline, YOU WILL NO LONGER HAVE ACCESS TO YOUR DATA IN GALAXY OR APOLLO, so plan accordingly.
What should I download?
We recommend that only the final products of analyses and workflows be saved. Downloading every dataset will put undue strain on the system and could cause it to fail sooner. Galaxy datasets can be saved directly from your history entry. To export your genomes from Apollo, run the Retrieve Data or Retrieve Data Fix tools (see our Dec. 17, 2023 update on using the Retrieve Data Fix tool). Download and save the history dataset called “Annotations and Sequence from Apollo” which contains your organism DNA sequence and annotations in GFF3 format.
What is the timeline?
The CPT Galaxy instance and Apollo will remain available until August of 2024, unless a major hardware failure forces us offline sooner. If the health of our system cannot be maintained, we may disable the ability to run new analyses before the August 2024 shutdown date to prolong data download functionality. We encourage you to register a user account at https://phage.usegalaxy.eu now for an easy transition.