Releases · GMOD/Apollo

06 Sep 19:43

nathandunn

2.0.7

2d82d56

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.

Assets 2

09 Dec 17:18

nathandunn

2.0.5

e05aa13

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]

Assets 2

10 Aug 01:59

nathandunn

2.0.4

e0aa79b

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]

Assets 2

15 Jun 16:35

nathandunn

2.0.3

3eebd58

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]

Assets 2

01 Apr 21:43

nathandunn

2.0.2

1bfa68d

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]

Assets 4

21 Dec 18:53

nathandunn

2.0.1

9c38352

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]

Assets 2

20 Aug 23:20

nathandunn

2.0.0

910277b

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]

Assets 2

10 Mar 14:58

cmdcolin

1.0.4

c8f7010

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

Assets 2