plugin NarrowPeak not found, please ensure the plugin was included in this JBrowse build

[mictadlo]

Hi @cmdcolin and @nathandunn , I added to

jbrowse {
    git {
        url= "https://github.com/GMOD/jbrowse"
        tag = "1.16.3-release"
        branch = "dev"
        alwaysPull = false
        alwaysRecheck = false
    }
    plugins {
        FeatureSequence {
           git = 'https://github.com/twsaari/FeatureSequence'
           branch = 'master'
           alwaysPull = "true"
        }
        NarrowPeak {
           git = 'https://github.com/cmdcolin/narrowpeak'
           branch = 'master'
           alwaysPull = "true"
        }        
    }
}

After log in to Apollo I got

Congratulations. Jbrowse is on the web.
Error Messages:
plugin NarrowPeak not found, please ensure the plugin was included in this JBrowse build

Please find the log files:

timestamp is utc, so its 10 hours behind

2019-04-17 23:27:10,184 [http-apr-8080-exec-15] INFO  apollo.JbrowseController  - Loading plugin: NarrowPeak details: {"git":"https://github.com/cmdcolin/narrowpeak","alwaysPull":"true","name":"NarrowPeak","location":"./plugins/NarrowPeak","branch":"master"}

these happened though

2019-04-17 23:27:10,301 [http-apr-8080-exec-25] DEBUG apollo.PreferenceService  - found organism in session org.bbop.apollo.Organism : 1739 so returning
| Error 2019-04-17 23:27:10,301 [http-apr-8080-exec-25] ERROR apollo.JbrowseController  - File not found: /jbrowse/sample_data/json/volvox/successfully_run

2019-04-17 23:28:05,427 [http-apr-8080-exec-54] WARN  apollo.PermissionService  - No user provided, please log in
2019-04-17 23:28:05,427 [http-apr-8080-exec-54] DEBUG apollo.PermissionService  - No permissions found on session
| Error 2019-04-17 23:28:05,428 [http-apr-8080-exec-54] ERROR apollo.AnnotatorController  - User does not have permissions for the site

database is running and all filesystems are mounted, is there any more info in the error.

build process sees the NarrowPeak plugin

Final plugins [WebApollo:[included:true], NeatHTMLFeatures:[included:true, linearGradient:0], NeatCanvasFeatures:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true], FeatureSequence:[git:https://github.com/twsaari/FeatureSequence, branch:master, alwaysPull:true], NarrowPeak:[git:https://github.com/cmdcolin/narrowpeak, branch:master, alwaysPull:true]]

when logging in to test, this occurred

23:45:06,759 [http-apr-8080-exec-15] ERROR errors.GrailsExceptionResolver  - StaleObjectStateException occurred when processing request: [POST] /apollo/sequence/getSequences/ - parameters:
name: 
start: 0
length: 50
sort: length
asc: false
clientToken: 135137287691226841166096031
Row was updated or deleted by another transaction (or unsaved-value mapping was incorrect) : [org.bbop.apollo.UserOrganismPreference#3615]. Stacktrace follows:
Message: Row was updated or deleted by another transaction (or unsaved-value mapping was incorrect) : [org.bbop.apollo.UserOrganismPreference#3615]
    Line | Method
->>  656 | $tt__getCurrentOrganismPreferenceInDB in org.bbop.apollo.PreferenceService
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
|    620 | $tt__getCurrentOrganismPreference     in     ''
|    133 | $tt__getCurrentOrganismForCurrentUser in     ''
|    183 | $tt__getSequences                     in org.bbop.apollo.SequenceController
|    198 | doFilter . . . . . . . . . . . . . .  in grails.plugin.cache.web.filter.PageFragmentCachingFilter
|     63 | doFilter                              in grails.plugin.cache.web.filter.AbstractFilter
|    449 | executeChain . . . . . . . . . . . .  in org.apache.shiro.web.servlet.AbstractShiroFilter
|    365 | call                                  in org.apache.shiro.web.servlet.AbstractShiroFilter$1
|     90 | doCall . . . . . . . . . . . . . . .  in org.apache.shiro.subject.support.SubjectCallable
|     83 | call                                  in     ''
|    383 | execute . . . . . . . . . . . . . . . in org.apache.shiro.subject.support.DelegatingSubject
|    362 | doFilterInternal                      in org.apache.shiro.web.servlet.AbstractShiroFilter
|    125 | doFilter . . . . . . . . . . . . . .  in org.apache.shiro.web.servlet.OncePerRequestFilter
|   1149 | runWorker                             in java.util.concurrent.ThreadPoolExecutor
|    624 | run . . . . . . . . . . . . . . . . . in java.util.concurrent.ThreadPoolExecutor$Worker
^    748 | run                                   in java.lang.Thread

2019-04-17 23:45:06,638 [http-apr-8080-exec-5] DEBUG apollo.PermissionService  - dataObject does not contain organism (may not be needed)
| Error 2019-04-17 23:45:06,759 [http-apr-8080-exec-15] ERROR errors.GrailsExceptionResolver  - StaleObjectStateException occurred when processing request: [POST] /apollo/sequence/getSequences/ - parameters:
name: 
start: 0
length: 50
sort: length
asc: false
clientToken: 135137287691226841166096031
Row was updated or deleted by another transaction (or unsaved-value mapping was incorrect) : [org.bbop.apollo.UserOrganismPreference#3615]. Stacktrace follows:
Message: Row was updated or deleted by another transaction (or unsaved-value mapping was incorrect) : [org.bbop.apollo.UserOrganismPreference#3615]
    Line | Method
->>  656 | $tt__getCurrentOrganismPreferenceInDB in org.bbop.apollo.PreferenceService
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
|    620 | $tt__getCurrentOrganismPreference     in     ''
|    133 | $tt__getCurrentOrganismForCurrentUser in     ''
|    183 | $tt__getSequences                     in org.bbop.apollo.SequenceController
|    198 | doFilter . . . . . . . . . . . . . .  in grails.plugin.cache.web.filter.PageFragmentCachingFilter
|     63 | doFilter                              in grails.plugin.cache.web.filter.AbstractFilter
|    449 | executeChain . . . . . . . . . . . .  in org.apache.shiro.web.servlet.AbstractShiroFilter
|    365 | call                                  in org.apache.shiro.web.servlet.AbstractShiroFilter$1
|     90 | doCall . . . . . . . . . . . . . . .  in org.apache.shiro.subject.support.SubjectCallable
|     83 | call                                  in     ''
|    383 | execute . . . . . . . . . . . . . . . in org.apache.shiro.subject.support.DelegatingSubject
|    362 | doFilterInternal                      in org.apache.shiro.web.servlet.AbstractShiroFilter
|    125 | doFilter . . . . . . . . . . . . . .  in org.apache.shiro.web.servlet.OncePerRequestFilter
|   1149 | runWorker                             in java.util.concurrent.ThreadPoolExecutor
|    624 | run . . . . . . . . . . . . . . . . . in java.util.concurrent.ThreadPoolExecutor$Worker
^    748 | run                                   in java.lang.Thread

What did I miss?

Thank you in advance,

Michal

[nathandunn]

@mictadlo Did you do an apollo clean-all and then a apollo deploy? If you could just dump the raw logs that would be best.

@cmdcolin Does this plugin work with the newer JBrowse?

[cmdcolin]

should work

[cmdcolin]

note that you could also just make your narrow peak file into a bigbed with the bigNarrowPeak schema, follow instructions here https://genome.ucsc.edu/goldenPath/help/bigNarrowPeak.html

bigbed support is natively supported without need for plugins