New Web Apollo release WA1.0.2(JB1.11.5)

[Monica Munoz-Torres]

Hello Everyone, 

We would like to announce a new Web Apollo release.

This is our first official mavenized release, and it includes a number of changes. If you currently have Web Apollo instances running, please be sure to read carefully through the updated documentation. Specially note: no more symlinking; please use property files instead.

This latest release can be downloaded from GitHub:

https://github.com/GMOD/Apollo/releases/latest

The Readme contains steps for a Quick Update to version 1.0.x (note changes): 

https://github.com/GMOD/Apollo/blob/master/README.md

Complete WebApollo installation and configuration instructions for 1.x are available at: 

http://webapollo.readthedocs.org

For a detailed account of all changes, please visit: 

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

These are a few highlighted changes:

Features: 

+ Added functionality for extending to downstream/upstream acceptor/donor splice sites

+ Added "revert" buttons on rows in history to allow one click change of state

+ Added "{" and "}" for navigating between top level features

+ Added feature coordinates to the "Get Sequence" (get_sequence) output

+ Added tool to split all isoforms into individual genes (RemoveIsoforms.java)

+ Added ability to hide track labels under "view".

+ Added ability to switch between light / dark background color schemes.

+ Added tool for fixing gene boundaries based on children transcripts (FixGeneBoundaries.java)

+ Added option to allow use of encrypted database but does not require it, and

+ Added ability to encrypt an unencrypted  database via encrypt_passwords.pl

+ Using javascript minimization for JBrowse+WebApollo to allow faster initial load time

+ Using Maven build system for deployment (See new installation guide listed above)

+ Integrate with TravisCI: https://travis-ci.org/GMOD/Apollo

+ Added ability to visualize latest changes, and menu items to changes and sequence-selection pages to the annotation screen, fixing memory issues from selectTrack.jsp and recentChanges.jsp pages.

+ alt/Option+click brings up Information Editor on annotated track.

+ Added webservices doc links to interface.

+ Added command line exporters for GFF3 files.

+ Using JBrowse 1.11.5

Bugfixes:

+ Fixed phase in GFF3 output

+ Disabled scrollToPreviousEdge/scrollToNextEdge if the feature is fully visible at the current zoom level

+ Included Chado libraries that were missing in 2014-04-03 release

+ Removed 'null' tracks from changes.

+ Menus use proper CSS pointer.

If you are new to Apollo, we suggest that you learn more about our software and its functionality by taking a tour of the Web Apollo Demo (http://genomearchitect.org/WebApolloDemo) and exploring the User Guide (http://genomearchitect.org/web_apollo_user_guide)

We look forward to receiving your questions and suggestions. 

Sincerely, 

The Web Apollo Development Team

--

Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory

Mailing Address:
Joint Genome Institute (400-0415)
for the US Department of Energy
2800 Mitchell Dr. Ste 100
Walnut Creek, CA 94598-1631

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