GMOD Apollo Versions Save

Features

• Add info icon with tooltip describing meaning of fmin and fmax in "Partial". @garrettjstevens. 2649.

Infrastructure Changes

• Upgrade Log4j to 2.19.0. Thanks @cmdcolin. 2654.
  • Due to this change, export of instructor reports is no longer available

Full change long for all versions can be found here: https://github.com/GMOD/Apollo/blob/develop/ChangeLog.md

Docker builds are on docker hub: https://hub.docker.com/r/gmod/apollo

Please review the documentation pages for more details: http://genomearchitect.readthedocs.io/en/latest/

Note: You can find a guide to upgrading existing Apollo installations here: https://genomearchitect.readthedocs.io/en/latest/Migration.html

Report issues if found. Active mailing list ([email protected]) and google group.

Features

• Update Docker container to use Ubuntu 20.04 as the base image (was 18.04). Thanks @christabone. 2645

Bug Fixes

• Fix typo in Docker docs. Thanks @christabone. 2638
• Use fmin and fmax instead of 3' and 5' in the UI when marking feature ends as partial. This more accurately reflects how Apollo stores the data about partials. 2646

Full change long for all versions can be found here: https://github.com/GMOD/Apollo/blob/develop/ChangeLog.md

Docker builds are on docker hub: https://hub.docker.com/r/gmod/apollo

Please review the documentation pages for more details: http://genomearchitect.readthedocs.io/en/latest/

Note: You can find a guide to upgrading existing Apollo installations here: https://genomearchitect.readthedocs.io/en/latest/Migration.html

Report issues if found. Active mailing list ([email protected]) and google group.

This release contains a fix that caused users to not be able to build due to a change to the Grails servers. See grails/grails-core#11825. If you are not able to upgrade Apollo to this version but still are experiencing build failures, you can update your BuildConfig.groovy file as in this PR: 2624.

Features

• Added method to upload bulk functional annotations from JSON in the interface. 2617,2618
• Added a "topLevel" option to the "getFeatures" web services endpoint that causes the endpoint to return top-level (e.g. gene) features. 2616

Bug Fixes

• Removed deprecation from SequenceController.sequenceByName. 2619
• Fix contextual menu for blastview tracks. Thanks @abretaud. 2621
• Make Python libraries installed globally in Docker image. 2622
• Update mavenRepo to fix error grails server error during build, see grails/grails-core#11825. 2624

Full change long for all versions can be found here: https://github.com/GMOD/Apollo/blob/develop/ChangeLog.md

Docker builds are on docker hub: https://hub.docker.com/r/gmod/apollo

Please review the documentation pages for more details: http://genomearchitect.readthedocs.io/en/latest/

Note: You can find a guide to upgrading existing Apollo installations here: https://genomearchitect.readthedocs.io/en/latest/Migration.html

Report issues if found. Active mailing list ([email protected]) and google group.

Features

• Added getAttributions method 2591 via @mbc32.
• Make getting track features by location optional to pull unique code 2600.
• Added additional websocket authentication support 2598.
• Added 'set optimal ORF' function 2129.

Bug Fix

• Provide better detection and fallback for detecting proper Grails version 2020.
• Bad WithOrFrom functional annotation evidence can hide display 2595.
• Fixed bad API doc 2605.
• Fix safari annotation panel layout 2603.

Infrastructure Changes

• Upgrade to JBrowse 1.16.11
• Removed server phone home 2614.

Full change long for all versions can be found here: https://github.com/GMOD/Apollo/blob/develop/ChangeLog.md

Docker builds are on docker hub:

https://hub.docker.com/r/gmod/apollo Please review the documentation pages for more details: http://genomearchitect.readthedocs.io/en/latest/

Note: You can find a guide upgrading existing Apollo installations here: https://genomearchitect.readthedocs.io/en/latest/Migration.html

Report issues if found. Active mailing list ([email protected]) and google group.

Official Release

2.6.3

Features

• Fix empty attribute list in annotation panel 2552.
• 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:

• 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.

Infrastructure Changes

• Removed travis in favor of GitHub Actions 2546.

Full change long for all versions can be found here: https://github.com/GMOD/Apollo/blob/develop/ChangeLog.md

Docker builds are on quay.io and docker hub:

https://quay.io/repository/gmod/apollo?tab=builds https://hub.docker.com/r/gmod/apollo Please review the documentation pages for more details: http://genomearchitect.readthedocs.io/en/latest/

Note: You can find a guide upgrading existing Apollo installations here: https://genomearchitect.readthedocs.io/en/latest/Migration.html

Report issues if found. Active mailing list ([email protected]) and google group.

RELEASE CANDIDATE 1

2.6.3-RC1

Features

• Fix empty attribute list in annotation panel 2552.
• 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.

Bug Fixes:

• 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

Infrastructure Changes

• Removed travis in favor of GitHub Actions 2546.

Full change long for all versions can be found here: https://github.com/GMOD/Apollo/blob/develop/ChangeLog.md

Docker builds are on quay.io and docker hub:

https://quay.io/repository/gmod/apollo?tab=builds https://hub.docker.com/r/gmod/apollo Please review the documentation pages for more details: http://genomearchitect.readthedocs.io/en/latest/

Note: You can find a guide upgrading existing Apollo installations here: https://genomearchitect.readthedocs.io/en/latest/Migration.html

Report issues if found. Active mailing list ([email protected]) and google group.

OFFICIAL

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

• Upgrade to JBrowse 1.16.10

Full change long for all versions can be found here: https://github.com/GMOD/Apollo/blob/develop/ChangeLog.md

Docker builds are on quay.io and docker hub:

https://quay.io/repository/gmod/apollo?tab=builds https://hub.docker.com/r/gmod/apollo Please review the documentation pages for more details: http://genomearchitect.readthedocs.io/en/latest/

Note: You can find a guide upgrading existing Apollo installations here: https://genomearchitect.readthedocs.io/en/latest/Migration.html

Report issues if found. Active mailing list ([email protected]) and google group.

RELEASE CANDIDATE 1 2.6.2-RC1

This is a minor release with bug fixes and feature changes.

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

• Upgrade to JBrowse 1.16.10

Full change long for all versions can be found here: https://github.com/GMOD/Apollo/blob/develop/ChangeLog.md

Docker builds are on quay.io and docker hub:

https://quay.io/repository/gmod/apollo?tab=builds https://hub.docker.com/r/gmod/apollo Please review the documentation pages for more details: http://genomearchitect.readthedocs.io/en/latest/

Note: You can find a guide upgrading existing Apollo installations here: https://genomearchitect.readthedocs.io/en/latest/Migration.html

Report issues if found. Active mailing list ([email protected]) and google group.

2.6.1 Official Release

This is a minor release with bug fixes and feature changes.

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.

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.

Full change long for all versions can be found here: https://github.com/GMOD/Apollo/blob/develop/ChangeLog.md

Docker builds are on quay.io and docker hub:

https://quay.io/repository/gmod/apollo?tab=builds https://hub.docker.com/r/gmod/apollo Please review the documentation pages for more details: http://genomearchitect.readthedocs.io/en/latest/

Note: You can find a guide upgrading existing Apollo installations here: https://genomearchitect.readthedocs.io/en/latest/Migration.html

Report issues if found. Active mailing list ([email protected]) and google group.

2.6.0 Official Release

Major features include:

• Removed popups for annotations in favor of annotator panel tabs 2334
• Implemented gene product and field provenance annotations with evidence and GFF3 export 2371, 2234, 2312, 2424
• 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
• Split out default GO Evidence Codes from ECO codes 2429

There are numerous other features, bug fixes and infrastructure changes as well. More changes can be found here: https://github.com/GMOD/Apollo/blob/develop/ChangeLog.md

Docker builds are on quay.io and docker hub:

https://quay.io/repository/gmod/apollo?tab=builds https://hub.docker.com/r/gmod/apollo Please review the documentation pages for more details: http://genomearchitect.readthedocs.io/en/latest/

Note: You can find a guide upgrading existing Apollo installations here: https://genomearchitect.readthedocs.io/en/latest/Migration.html

Report issues if found. Active mailing list ([email protected]) and google group.

AWS EC2 Community images of Apollo 2.6.0 will be available within the N. Virginia and California regions minimally. Please request on the forum or ticketing system if more are needed.