2.5.0

2.5.0 Official Release

Major features include:

• Moved blat / blast search to its own tab 2259
• Allow creation of annotations from blat features 2225
• On upload of fasta file execute faToTwoBit if present to create searchable blat file 2262
• Allows history tracking for non-structural edits 2246

There are numerous bug fixes and web-service fixes.
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 2.5.0 will be available within the N. Virginia and California regions minimally. Please request on the forum or ticketing system if more are needed.

2.4.1

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

2.4.0

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:

• 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

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

Active mailing list ([email protected]) and archive.

2.3.1

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 ([email protected]) 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

2.3.0 JB-1.16.2

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 ([email protected]) and archive.

2.2.0 JB#maint/1.15.4-release

Apollo 2.2.0 Official Release

Major features of this release are:

• webpack support added
• update to the newest JBrowse (1.15) to support WebPack added

Some other improvements:

Features

• Add ability to annotate terminators 1954
• Allowed removal of ALL user permissions (instead of deleting) to inactivate 777

Bug Fixes

• Fixed by where lowercase reference sequence does not translate correctly in 'Get Sequence' output 1944
• Fixed problem where removing an available status type caused an error 1909
• Fixed bug where a logged-in link location was ignored when passed in by copying the logged in URL 1982
• Fixed bug where insertion and deletion details did not come up in the Annotator Panel when clicked 1984

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

Note You will need to install node 6 or better.
Note If updating your jbrowse settings from previous versions in apollo-config.groovy you will need to set the JBrowse to use the currently tagged version or similar. If this is commented out, however, the default will work.
Note If upgrading a pre-existing version (instead of downloading a clean one), use ./apollo clean-all first and make sure your configuration matches the default listed above.

The complete change log can be found at: https://github.com/GMOD/Apollo/blob/master/ChangeLog.md

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 ([email protected]) and archive.

2.1.0-JB#maint/1.12.5-apollo

2.1.0 Official Release

Some of the new features include:

• Added ability to annotate a variant from VCF evidence tracks 1892
• Allow forced assignment of transcript to a gene #1851
• Added proper Instructor and Organism Admin permission level #1178
• Indicate start / stop codons with color #1852
• Set the default biotype on track #1861

Some important bug fixes:

• Prevents setting bad translation starts and ends #1838
• Fixed descriptor leak when loading bulk loading GFF3 #1187
• Fixed adding ability to create sequence alterations of uneven length #1883
• Fixed problem where canonical splice-sites were not recognized if sequence was being shown in lower-case #1879
• In some cases when the name store is not properly configured, the location is not remembered #1895

Note You will need to install node 6 or better.
Note If updating your jbrowse settings from previous versions in apollo-config.groovy you will need to set the JBrowse to use the currently tagged version or better. If this is commented out, however, the default will work.
Note Some issues with new tomcat and addStore / addTracks RFC 7230 and RFC 3986. See http://genomearchitect.readthedocs.io/en/latest/Setup.html?highlight=RFC#json-in-the-url-with-newer-versions-of-tomcat

The complete change log can be found at: https://github.com/GMOD/Apollo/blob/master/ChangeLog.md

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 ([email protected]) and archive.

Apollo2.0.8(JB#d3827c)

Official Release

Apollo 2.0.8

Some of the new features include:

• added ability to annotate canvas BAM tracks
• expanded track services
• support for indexed FASTA as a reference sequence

Some important bug fixes:

• numerous fixes to track web services
• fixed numerous build issues

Note You will need to install node 6 or better.
Note If updating your jbrowse settings from previous versions in apollo-config.groovy you will need to set the JBrowse to use the currently tagged version or better. If this is commented out, however, the default will work.
Note Some issues with new tomcat and addStore / addTracks RFC 7230 and RFC 3986. See http://genomearchitect.readthedocs.io/en/latest/Setup.html?highlight=RFC#json-in-the-url-with-newer-versions-of-tomcat

The complete change log can be found at: https://github.com/GMOD/Apollo/blob/master/ChangeLog.md

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 ([email protected]) and archive.

Apollo2.0.7(JB#9d765ae)

Apollo 2.0.7 Official Release

Some of the new features include:

• Support for categories in Track Panel
• Draggable BAM tracks support color by strand
• Removal of bower in favor of npm to install JBrowse
• Add the ability to upload organism sequence data and track data to a remote Apollo instance via Apollo Web Services.

Some important bug fixes:

• Improved code dealing with preferences.
• Fix a bug that prevented Apollo from generating URLs appropriately - pipes were not being encoded properly on all platforms.

Note You will need to install node 5 or better.
Note If updating your jbrowse settings from previous versions in apollo-config.groovy you will need to set the JBrowse to use the currently tagged version or better. If this is commented out, however, the default will work.

The complete change log can be found at: https://github.com/GMOD/Apollo/blob/master/ChangeLog.md

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 ([email protected]) and archive.

Apollo2.0.5(JB#9334e76fd)

Apollo 2.0.5 Official Release

Some of the new features include:

• Numerous UI and performance improvements, including easier navigation between annotated elements via the Annotator Panel.
• Better server and client-side reporting.
• Upgrade to Java 8 / GWT 2.8, and updated JBrowse (use ./apollo clean-all or install from an formal release download)
• It is now possible to also include metadata on import.

Some important bug fixes:

• Import script were logging preferences unnecessarily.
• Improved security for non-public genomes.
• Fixed for going between logged-out mode and the Annotator Panel while retaining history.
• Improved display of sequence over the annotation after moving the annotation to the opposite strand.
• Users will see a warning when it is not possible to create an intron with canonical splice sites in the selected region.

The complete change log can be found at: https://github.com/GMOD/Apollo/blob/master/ChangeLog.md

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:
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 [email protected]