GMOD/Apollo: Apollo2.1.0(JB#d3827c)

2.1.0 Official Release

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

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 (apollo@lists.lbl.gov) and [archive](http://gmod.827538.n3.nabble.com/Apollo-f815553.html).