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GMOD / jbrowse

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.
http://jbrowse.org
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JBrowse 1.163 plugin Dynamix not found #1360

Closed shihabdider closed 5 years ago

shihabdider commented 5 years ago

I'm trying to install and run the Dynamix plugin. I followed the instructions here. Moved the plugin to the plugins folder, ran setup.sh (without any errors), activated the plugin in the jbrowse.conf and got the following error:

plugin Dynamix not found, please ensure the plugin was included in this Jbrowse build

Weird thing is, other plugins don't seem to raise the error (e.g NeatCanvasFeatures, MyVariantViewer)

cmdcolin commented 5 years ago

That error message is often due to trying to use a plugin with a minimized non-dev release of jbrowse. I tested cloning https://git.embl.de/monfort/dynamix.git into the plugins folder of a git repo (I named the folder Dynamix, case matters) of jbrowse (a git clone or dev version of jbrowse is needed) and ran setup.sh and added the plugin to the configuration and it seemed to work.

shihabdider commented 5 years ago

Unfortunately, I think I'm already on the dev branch:

$ git checkout dev
M   yarn.lock
Already on 'dev'

And I don't think I got tripped up by the case:

[plugins]$ ls
CategoryUrl  DebugEvents  Dynamix  HideTrackLabels  MyVariantViewer  NeatCanvasFeatures  NeatHTMLFeatures  RegexSequenceSearch

...and in the jbrowse.conf:

[ plugins.Dynamix ]
location = plugins/Dynamix
cmdcolin commented 5 years ago

If you open your setup.log it should say that it found Dynamix in the build

...
jbrowse-glob-loader: adding plugin module HideTrackLabels/main
jbrowse-glob-loader: adding plugin module Dynamix/widgets/masterWidget
jbrowse-glob-loader: adding plugin module Dynamix/widgets/dxTrackGroupWidget
jbrowse-glob-loader: adding plugin module Dynamix/main
jbrowse-glob-loader: adding plugin module Dynamix/dxTrackGroup
jbrowse-glob-loader: adding plugin module DebugEvents/main
jbrowse-glob-loader: adding plugin module CategoryUrl/main
jbrowse-glob-loader: discovered a total of 247 modules
jbrowse-glob-loader: skipping entry point module JBrowse/standalone
...
shihabdider commented 5 years ago

Yep, it does indeed say that:

$ webpack
clean-webpack-plugin: /data/jbrowse/dist has been removed.
jbrowse-glob-loader: building 205 JBrowse modules
jbrowse-glob-loader: adding plugin module RegexSequenceSearch/View/SearchSeqDialog
jbrowse-glob-loader: adding plugin module RegexSequenceSearch/Store/SeqFeature/RegexSearch
jbrowse-glob-loader: adding plugin module RegexSequenceSearch/main
jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/View/Track/NeatFeatures
jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/main
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/Track/NeatFeatures
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/UnprocessedTranscript
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Segments
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/ProcessedTranscript
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Gene
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Box
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/main
jbrowse-glob-loader: adding plugin module MyVariantViewer/View/Track/CanvasFeatures
jbrowse-glob-loader: adding plugin module MyVariantViewer/View/FeatureGlyph/Diamond
jbrowse-glob-loader: adding plugin module MyVariantViewer/Store/SeqFeature/Variants
jbrowse-glob-loader: adding plugin module MyVariantViewer/Store/SeqFeature/Genes
jbrowse-glob-loader: adding plugin module MyVariantViewer/Store/SeqFeature/Genes_v3
jbrowse-glob-loader: adding plugin module MyVariantViewer/Store/Names/REST
jbrowse-glob-loader: adding plugin module MyVariantViewer/main
jbrowse-glob-loader: adding plugin module HideTrackLabels/main

jbrowse-glob-loader: adding plugin module Dynamix/widgets/masterWidget
jbrowse-glob-loader: adding plugin module Dynamix/widgets/dxTrackGroupWidget
jbrowse-glob-loader: adding plugin module Dynamix/main
jbrowse-glob-loader: adding plugin module Dynamix/dxTrackGroup

jbrowse-glob-loader: adding plugin module DebugEvents/main
jbrowse-glob-loader: adding plugin module CategoryUrl/main
jbrowse-glob-loader: discovered a total of 231 modules
jbrowse-glob-loader: skipping entry point module JBrowse/standalone
jbrowse-glob-loader: skipping entry point module JBrowse/main
jbrowse-glob-loader: skipping entry point module JBrowse/standalone
jbrowse-glob-loader: skipping entry point module JBrowse/main

(Line breaks added for emphasis)

cmdcolin commented 5 years ago

if that's true I would clear browser cache and refresh :)

shihabdider commented 5 years ago

Man I can't believe that was it! It seems to be working now.

Thanks so much @cmdcolin!