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  • Fixes Mac Drag Error by upgrading JBrowse default to 1.16.6 GMOD/jbrowse#1397
  • Makes organisms and groups searchable. 2081
Assets 2

@nathandunn nathandunn released this Jun 28, 2019 · 10 commits to develop since this release

2.4.0 OFFICIAL RELEASE

Major features include:

  • GO Annotations with GPAD2 export
  • Upload file to server to create genome annotations and tracked
  • UI support for manual variant effect prediction

All bug fixes and features detailed here:

https://github.com/GMOD/Apollo/blob/develop/ChangeLog.md#240

Docker builds are on quay and docker hub:

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

Please open a GitHub issue if you find any problems: https://github.com/GMOD/Apollo/issues/

Active mailing list (apollo@lists.lbl.gov) and archive.

Assets 2
Jun 21, 2019
bumped for RC2
Jun 21, 2019
updated version and change log

@nathandunn nathandunn released this Feb 19, 2019 · 152 commits to master since this release

2.3.1 Official Release

Many bug fixes and some minor enhancements. Many thanks to the community for reporting, testing, and fixing these issues.

https://github.com/GMOD/Apollo/blob/master/ChangeLog.md#231

To test in Docker:

docker run -it -p 8888:8080 quay.io/gmod/docker-apollo:2.3.0 -v /path/to/jbrowse/directories:/data/
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

Please open a GitHub issue if you find any problems: https://github.com/GMOD/Apollo/issues/

Active mailing list (apollo@lists.lbl.gov) and archive.

Bug Fixes

  • Fixed issue when dragging features to resize was not providing an indicator box 1988
  • Fixed issue when sequence alterations were not rendering the full height of the sequence track 2049
  • Making organisms obsolete should remove associated permissions 2043
  • User-created features taken from split reads should create features with introns 2036
  • Should indicate split reads properly in evidence 20342054
  • Temporary files not removed during export of GFF3 or other file types 1966
  • Fixed issue where you could not alter an isoform after deleting a gene name 1961
  • Fixed some minor issues associated with sequence alterations 1497
  • Multiple owners tagged on GFF3 export 29
  • Setting gene description puts UcA into a bad state 2056
  • Fixes plugin inclusion error by reverting prior fix 2055

Minor Features

  • Allowed duplication of organism from the Organism Panel 1968
  • Allows making an organism obsolete 1967
  • Create a filter and flag for inactive users 1937
  • Allowed deletion of feature from the Sequence and Annotator Panels 2040
  • Allow export of orig_id as an optional attribute 2002
Assets 2
Feb 19, 2019
retagged
Feb 17, 2019
added instructions
Feb 15, 2019
bumping version

@nathandunn nathandunn released this Feb 5, 2019 · 205 commits to master since this release

2.3.0 Official Relase

Features

  • Moved to Neat Features as the default 2021
  • Moved to JBrowse 1.16.2 by default 1988, which also fixed track styling issues #1942

Other bug fixes and features added as well: https://github.com/GMOD/Apollo/blob/master/ChangeLog.md

To test in Docker:

docker run -it  -p 8888:8080 quay.io/gmod/docker-apollo:2.3.0 -v /path/to/jbrowse/directories:/data/

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

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

Please open a GitHub issue if you find any problems: https://github.com/GMOD/Apollo/issues/

Active mailing list (apollo@lists.lbl.gov) and archive.

Assets 2
Jan 29, 2019
bumped version
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