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

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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



-----------------------
Please receive our apologies in advance if you have received this message more than once. In an attempt to spread the word, we may have inadvertently reached to you through two or more mailing lists. - BBOP.

--
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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