[Gmod-ajax] Apollo 2.1.0 released / see you at Galaxy / BOSC 2018

[Nathan D. <nat...@lb...>]

1 - Apollo 2.1.0 has been released!  https://github.com/GMOD/Apollo/releases/tag/2.1.0 <https://github.com/GMOD/Apollo/releases/tag/2.1.0>

2 - Members of the Apollo and JBrowse teams will be at the Galaxy BOSC conference at the end of next week with an Apollo talk and poster and a few birds of a feather sessions for JBrowse and a Thursday / Friday hackathon with both teams there as well as tons of GMODers and of course lots of brilliant Galaxy folks: https://gccbosc2018.sched.com/ <https://gccbosc2018.sched.com/>.  It would be a great time to add features, get bugs fixed, etc. 

Please reply to the lists directly or email me if you have any further questions or project ideas. 

Cheers,

The Apollo team




= More on the Apollo 2.1.0 release = 

Thanks for the testing, patching, requests and bug reporting.

Other availability:
- There should be an Amazon Web Service Community image available on most AWS zones called “Apollo 2.1.0 Template”
- I updated our docker image to support 2.1.0 as a starting point for your own docker integrations: http://github.com/GMOD/docker-apollo <http://github.com/GMOD/docker-apollo>  It is built on both docker hub https://hub.docker.com/r/gmod/apollo/ <https://hub.docker.com/r/gmod/apollo/> (still building)  and quay https://quay.io/repository/gmod/docker-apollo?tab=tags <https://quay.io/repository/gmod/docker-apollo?tab=tags> (working now).

Some of the new features include:

Added ability to annotate a variant from VCF evidence tracks 1892 <https://github.com/GMOD/Apollo/pull/1892>
Allow forced assignment of transcript to a gene #1851 <https://github.com/GMOD/Apollo/pull/1851>
Added proper Instructor and Organism Admin permission level #1178 <https://github.com/GMOD/Apollo/issues/1178>
Indicate start / stop codons with color #1852 <https://github.com/GMOD/Apollo/pull/1852>
Set the default biotype on track #1861 <https://github.com/GMOD/Apollo/issues/1861>
Some important bug fixes:

Prevents setting bad translation starts and ends #1838 <https://github.com/GMOD/Apollo/issues/1838>
Fixed descriptor leak when loading bulk loading GFF3 #1187 <https://github.com/GMOD/Apollo/pull/1887>
Fixed adding ability to create sequence alterations of uneven length #1883 <https://github.com/GMOD/Apollo/issues/1883>
Fixed problem where canonical splice-sites were not recognized if sequence was being shown in lower-case #1879 <https://github.com/GMOD/Apollo/issues/1879>
In some cases when the name store is not properly configured, the location is not remembered #1895 <https://github.com/GMOD/Apollo/issues/1895>
Note You will need to install node 6 or better <https://nodejs.org/en/download/package-manager/>.
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 <https://github.com/GMOD/Apollo/blob/master/sample-postgres-apollo-config.groovy#L113>. If this is commented out, however, the default will work <https://github.com/GMOD/Apollo/blob/master/grails-app/conf/Config.groovy#L388-L433>.
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 <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 <https://github.com/GMOD/Apollo/blob/master/ChangeLog.md>
Please review the documentation pages for more details: http://genomearchitect.readthedocs.io/en/stable/ <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 <http://genomearchitect.readthedocs.io/en/stable/Migration.html>
Please open a GitHub issue if you find any problems: https://github.com/GMOD/Apollo/issues/ <https://github.com/GMOD/Apollo/issues/>
Active mailing list (ap...@li... <mailto:ap...@li...>) and archive <http://gmod.827538.n3.nabble.com/Apollo-f815553.html>.