← Back to news

UseGalaxy.eu Apollo Update

By hexylena

May 19, 2021

The GGA team has updated UseGalaxy.eu's Apollo (collaborative genome annotation editor) to 2.6.3 from 2.5.0. Check out the changelog copied below.

Not yet using apollo for your genome annotation needs? Come talk to us as GCC2021 where we'll have a couple of training modules covering the system's use.

2.6.3

Features

  • Added ability to use posts to sequence methods 2555.
  • Added system info web service 2557.
  • Add "merged from" comment to merged in transcript and gene 2567.
  • Added support for "obsolete", and partials in the interface for GFF3s 2573.
  • Allow overlap filter to be configurable 2582.

Bug Fixes:

  • Fix empty attribute list in annotation panel 2552.
  • Bad coordinate value in genomic element details screen in annotator panel 2559.
  • Web services indicated user had no organism permissions when checking the login 2554.
  • Vcf reads as ISO-8859-1 instead of UTF-8 from reader mangling some symbols. 2498.
  • Added security fixes for web services. 2564, 2587.
  • In some cases web services tries to create a preference which results in incorrect results 2580.
  • For the track service, the overlap filter is too restrictive when converting NCList to JSON 2586.
  • History track names for Gene Produce and Provenance were being cast as GO 2590.

Infrastructure Changes

  • Removed travis in favor of GitHub Actions 2546.

2.6.2

Features

  • Add option to suppress calculation of non-canonical splice site 2509.
  • Added the ability to sync the gene and transcript name with the click of a button 2519.
  • Added organism and species to menus 2537.
  • Added UUID lookup and link 2539.
  • Added status filter for recent annotations 2543.
  • Add feature name loc to loadLink 2544.
  • loc loadLink now supports UUID and ID popup provides link 2549.

Bug Fixes

  • BLAT search should send annotation creation results to the proper reference sequence 2514.
  • Properly handle Shine_Dalgarno sequences when added as part of gene model 2515.
  • Now able to resize terminators by dragging 2521.
  • Added missing GO annotations 2535.
  • findAllOrganism webserver failed when user is not an admin and no session is present 2540.
  • Provide minor UI and bug fixes 2548.

Infrastructure Changes

2.6.1

Infrastructure Changes

  • Upgrade to JBrowse 1.16.9 / 2489.
  • Fixed Python dependency for Travis for BioPython (3.7) and upgraded to Xenial 2493.
  • Updated internal Docker Python script to add to use the Apollo 4.2.3 library.
  • Shows and hide annotation detail panels on demand so list is not obscured 2538

Bug Fixes

  • Tabix upload of tracks was not including the index file 2487.
  • Fasta file was displaying the wrong file formats 2486.
  • Removed unused database migration script causing issues with mysql d50f061887.
  • Allow addition of a controller vocabulary for Gene Product Description 2488.
  • Fixed ECO evidence code links 2491.
  • Fixed load-link urls 2500.

2.6.0

Features

  • Remove popups for annotations in favor of annotator panel 2334
  • Added 2 more pseudogenic SO terms and several more non-coding RNA terms and updated interfaces to reflect these 2475
  • Implemented gene product and field provenance annotations with evidence and GFF3 export 2371, 2234, 2312, 2424
  • Added name and type to top of annotation details 2423
  • Added GO Annotations to GFF3 export and extended to transcript 2400
  • loadLink can take name of gene in evidence (if JBrowse names have been processed) 2444
  • Add alias to user interface and GFF3 export 2277
  • Add help menu feedback 2344
  • Allows for better performance when a large number of annotations are present 2477
  • Show genome features in current view 2346
  • Remove sequence lookup at the top 2407
  • Provide better security and feedback when trying to export with insufficient permissions 2431
  • Split out default GO Evidence Codes from ECO codes 2429
  • Added more info (e.g, JBrowse and general settings) to the about window and is visible on login 47f469f7

Infrastructure Changes

Bug Fixes

  • Open by uniquename to get only the results of the name we are interested in 2338
  • Fixed ability to add multiple BAMs at once 2352
  • Fixed export of non-coding RNA if exon not present 2353
  • Removed sequence panel lookup 2388
  • Annotator/updateFeature should store history properly 2390
  • Makes sure that parent directory exists when unpacking 2437
  • Fixed bug when decompressing gff3.gz data when adding a new track 2434
  • Fixed boolean environment options being interpreted correctly be31b81f7