Apollo2.0.4(JB1.12.2-apollo)

Apollo 2.0.4 Official Release

Some of the new features include:

• Users may download genomic sequences from highlighted regions.
• Information from parent features can be retained when loading transcripts onto the 'User-created Annotations' area using the command line.
• REMOTE_USER authentication and pluggable authentication modules now available.
• Ability to enter pre-specified (canned) valies for Attributes in the 'Information Editor', similar to canned Comments.
• Upgraded to Grails 2.5.5.

Some important bug fixes:

• Fixed multiple errors in add_transcript_from_gff3_to_annotations.pl script.
• Fixed service timeout / disconnection silent error.
• Fixed several deployment installation issues.

Full change log is here: https://github.com/GMOD/Apollo/blob/master/ChangeLog.md

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

A quick-start guide for Web Apollo 2.0 is available at:

http://genomearchitect.readthedocs.io/en/latest/Apollo2Build.html

• Note: You can find a guide for migrating existing annotations from Web Apollo 1 here.

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

Active mailing list [email protected]

Apollo2.0.3(JB1.12.2-apollo)

Official Release

Apollo 2.0.3

Some of the new features include:

• Chado export
• Ability to change genomic feature type after creating annotation
• Upgrade to JBrowse version 1.12.2-apollo
• Ability to annotate multiple organisms at the same time

Some important bug fixes:

• Canvas tracks now able to annotate all features types
• Comment not restricted to 256 characters
• Undo operations on a pseudogene caused an error

Full change log is here: https://github.com/GMOD/Apollo/blob/master/ChangeLog.md

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

A quick-start guide for Web Apollo 2.0 is available at:

http://genomearchitect.readthedocs.io/en/latest/Apollo2Build.html

• Note: You can find a guide for migrating existing annotations from Web Apollo 1 here.

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

Active mailing list [email protected]

WA2.0.2(JB1.11.6)

Apollo 2.0.2 - Official Release
Some of the new features include:

• Numerous performance and user interface improvements
• Expanded web services documentation and examples

Some important bug fixes:

• Added back alternate translation table support
• Fixed bug having to do with navigating history with split and merged transcripts
• Fixed performance and migration errors with MySQL

Full change log is here: https://github.com/GMOD/Apollo/blob/master/ChangeLog.md

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

A quick-start guide for Web Apollo 2.0 is available at:

http://genomearchitect.readthedocs.io/en/latest/Apollo2Build.html

• Note: You can find a guide for migrating existing annotations from Web Apollo 1 here.

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

Active mailing list [email protected]

WA2.0.1(JB1.11.6)

Apollo 2.0.1 Official release

Some of the new features include:

• Numerous performance and user interface improvements
• Expanded web services documentation and examples
• Ability to view native track list (categories and facets)
• Full support of HTTPS

Some important bug fixes

• Feature merge and splits are properly calculated when feature boundaries change
• Allow for very long feature names
• Fixed integration between track list and side-panel

Full change log is here: https://github.com/GMOD/Apollo/blob/master/ChangeLog.md

Please review the documentation pages for more details: http://webapollo.readthedocs.org/en/latest/

A quick-start guide for Web Apollo 2.0 is available at:

http://genomearchitect.readthedocs.io/en/2.0.1/Apollo2Build/

• Note: You can find a guide for migrating existing annotations from Web Apollo 1 here.

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

Active mailing list [email protected]

WA2.0.0(JB1.11.6)

This is the first release of Apollo 2, and it is a major rewrite of the Apollo 1.0.x backend, focused on making the framework more scalable and interoperable while maintaining the core functionality that annotators have come to expect. Apollo 2 also brings new functionality that continues to improve the user experience.

Some of the new features include:

• Multi-organism support.
• Organism-level permissions.
• Alternate side-panel view for annotations, sequences, and user management.
• Reporting, including customizable reports.
• Single database integration (MySQL, PostgreSQL, Oracle, H2).
• Websocket implementation.
• Simplified configuration / install.

Please review the documentation pages for more details: http://webapollo.readthedocs.org/en/latest/

A quick-start guide for Web Apollo 2.0.0 is available at:
http://webapollo.readthedocs.org/en/latest/Apollo2Build.html

• Note: You can find a guide for migrating existing annotations from Web Apollo 1 here.

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

Active mailing list [email protected]

WA1.0.4(JB1.11.6)

Important Notes

• The GOLR server URL changed to "http://golr.geneontology.org/solr/". If not updating to 1.0.4, you can still patch it manually.
• The default for user-based database is now encrypted (see sample_config.xml). If you have an "unencrypted" database, the options have changed for adding users using tools/users/add_users.pl (-x for non-encrypted). You should not need to change your config.xml.
• If updating tag using an existing git repository, make sure to use "./apollo clean-all" before deploying.
• If updating pre-1.0, remove symlinks!
• Numerous small bug fixes and features implemented.

For a detailed account of all changes, please see:
https://github.com/GMOD/Apollo/blob/master/ChangeLog.md

Readme for a quickstart (note changes):
https://github.com/GMOD/Apollo/blob/master/README.md

Please see the Quick-Install guide for full setup details: http://webapollo.readthedocs.org/en/latest/Quick_start_guide/

PDF guide generated from readthedocs https://www.dropbox.com/s/31er7sfidoq5whw/WebApollo.pdf?dl=1

WA1.0.3(JB1.11.5)

Numerous bug fixes.

For a detailed account of all changes, please see: https://github.com/GMOD/Apollo/blob/master/ChangeLog.md

Readme for a quickstart (note changes): https://github.com/GMOD/Apollo/blob/master/README.md

Please see the QuickInstall guide for full setup details: http://webapollo.readthedocs.org/en/latest/Quick_start_guide/

WA1.0.2(JB1.11.5)

• Fixed caching bug #91.
• Updated UI #52 and #19 .

First official mavenized release. NOTE: no more symlinking. Please use property files instead.

Change log: https://github.com/GMOD/Apollo/blob/master/ChangeLog.md

Readme for a quickstart (note changes): https://github.com/GMOD/Apollo/blob/master/README.md

Please see the QuickInstall guide for full setup details: http://webapollo.readthedocs.org/en/latest/Quick_start_guide/

WA1.0.1(JB1.11.5)

First official mavenized release. NOTE: no more symlinking. Please use property files instead.

Change log: https://github.com/GMOD/Apollo/blob/master/ChangeLog.md

Readme for a quickstart (note changes): https://github.com/GMOD/Apollo/blob/master/README.md

Please see the QuickInstall guide for full setup details: http://webapollo.readthedocs.org/en/latest/Quick_start_guide/