Issue loading sequences in apollo with plugins

[hexylena]

I was trying to install @cmdcolin's GCContent plugin for every genome in our Apollo instance, per a PI request.

I saw

| Error Exception in thread "Thread-13" 
| Error java.lang.ClassCastException: org.codehaus.groovy.runtime.GStringImpl cannot be cast to java.lang.String
| Error         at org.codehaus.groovy.grails.project.compiler.GrailsProjectWatcher.run(GrailsProjectWatcher.java:114)

in the console whilst running ./apollo devmode. Every request for sequence data starts to 404.

• I've tried including just the plugin in annot.json, no build error, sequence is visible.
• As soon as I add the track, I get the casting exception and no sequence is visible.

{                                                                                                                                          
   "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",                                                                                       
   "type" : "GCContent/View/Track/GCContentXY",                                                                                            
   "label" : "GC Content XY",                                                                                                              
   "storeClass" : "JBrowse/Store/Sequence/StaticChunked",                                                                                  
}                                                                                                                                        

is the configuration of the track.

[cmdcolin]

There shouldn't be any problems using the plugin if it's setup right (normally just add plugin to annot.json, drop files in web-app/jbrowse/plugins/GCContent, and you're set).

If you are "compiling" the plugin in release mode, that I would use "apollo release", that will recursively go over the plugins in the jbrowse plugins directory and optimize the build

[hexylena]

Progress....

With plugin, the sequence request is being made to

http://localhost:8080/apollo/jbrowse/plugins/WebApollo/json/seq/cf3/8c8/ee/Miro-0.txt

without, it goes to

http://localhost:8080/apollo/jbrowse/data/seq/cf3/8c8/ee/Miro-0.txt

[hexylena]

Setting:

"urlTemplate" : "../../../data/seq/{refseq_dirpath}/{refseq}-",

fixes the issue completely (though it's a bit unintuitive)