Howdy all!
We have now released fully updated and tested workflows for the Structural and Functional workflows on CPT Galaxy, as well as the other Apollo bridge workflows for loading custom tracks.
We have also updated our training material site to include the new UI for both Galaxy and Apollo. Please take a look here if you are unfamiliar with the system or need a refresher. The Annotation in Apollo tutorial covers most of the major UI changes.
Many of the changes were to correctly format data for upload into the newest version of Apollo (2.6.1) or to ensure that the tools were configured to correctly run with Python 3 as Galaxy has made the change for it’s base requirements. Many toolshed tools may have been updated as well, to ensure compatibility.
Structural Workflow v2020.07:
- Organism Common Name is now set through an input entry field rather than in the Create or Update Organism tool at the bottom of the workflow invocation.
- Naïve ORF caller/Six Pack minimum gene length reduced from 30 amino acids to 25
- ShineFind tool changed to have search window defined by minimum/maximum lengths for gap between end of Shine-Dalgarno sequence and the start of a CDS
- Prep GFF3 For Apollo tool created to clean input into the JBrowse tool to ensure proper structure of GFF to display in Apollo
- JBrowse updated to use 1.16.8
- Apollo tools updated to use python-apollo library 4 .2.9
- Input is now a combined GFF+FASTA file instead of separate annotation and sequence files to match how data is retrieved from Apollo 2.6.1, the workflow includes the splitting tool
- NCBI BLASTp on NR Database filtered to only phage taxonomic IDs, dropped TAXID 2 (Bacteria)
- NCBI BLASTp on CPT Canonical Database rolled back to previous hand curated database from 2019 instead of taxid filtered NR
- Prep GFF3 For Apollo tool created to clean input into the JBrowse tool to ensure proper structure of GFF to display in Apollo
- JBrowse updated to use 1.16.8
- Apollo tools updated to use python-apollo library 4 .2.9
The CPT Galaxy team thanks you for your patience and understanding as we have rolled these updates out, please reach out to us if you have any issues or questions!