Re: [Gmod-ajax] jbrowse1.16.3 plugin not found

[Colin <col...@gm...>]

No worries

One other note, I think Hans had mentioned there might be some
compatibility issue between this plugin and the latest version of JBrowse
due to some upgrades that were made to the VCF parser. If you find this can
you document it?

Thanks

-Colin

On Thu, Feb 28, 2019 at 3:20 PM thomas <
tsi...@re...> wrote:

> Damn! That's what it was. It works now. Thanks very much for your help and
> sorry to have bothered you with such a rookie mistake.
>
> Best,
>
> Thomas
> On 2019-02-28 12:02 p.m., Colin wrote:
>
> Have you tried clearing browser cache and refreshing by chance?
>
>
>
> -Colin
>
> On Thu, Feb 28, 2019 at 2:36 PM thomas <
> tsi...@re...> wrote:
>
>> Hi Colin,
>>
>>
>> Thanks for your prompt answer and your help.
>>
>> I effectively use the JBrowse-1.16.3-dev.zip
>> <https://github.com/GMOD/jbrowse/archive/1.16.3-release.zip>
>> (jbrowse-1.16.3-release once unzipped, sorry for the confusion). I also
>> tried to build from source (git clone https://github.com/GMOD/jbrowse)
>> but although the setup runs fine, the plugin still fails to load (the
>> browser works fine without any plugin listed in jbrowse.conf).
>>
>> The plugins seems to be taken into account during setup during as shown
>> log file (line ~50):
>>
>>
>> $ webpack
>> clean-webpack-plugin: /var/www/jbrowse/dist has been removed.
>> jbrowse-glob-loader: building 205 JBrowse modules
>> jbrowse-glob-loader: adding plugin module
>> VariantEffectPlugin/View/Track/CanvasEffectVariants
>> jbrowse-glob-loader: adding plugin module
>> VariantEffectPlugin/View/Track/_VariantDetailMixin
>> jbrowse-glob-loader: adding plugin module VariantEffectPlugin/main
>> 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 HideTrackLabels/main
>> jbrowse-glob-loader: adding plugin module DebugEvents/main
>> jbrowse-glob-loader: adding plugin module CategoryUrl/main
>> jbrowse-glob-loader: discovered a total of 223 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
>> Hash: 4c7633339ca7b9824f57
>> Version: webpack 4.26.1
>> Time: 41529ms
>> Built at: 02/28/2019 6:52:02 PM
>>
>>
>> the log file is attached to this message as well as a screen shot of my
>> browser (with the error message).
>>
>> Thanks again for your help.
>>
>>
>> Best,
>>
>>
>> Thomas
>>
>>
>>
>>
>> On 2019-02-28 10:33 a.m., Colin wrote:
>>
>> That looks about right, wondering are you using the "-dev" version of the
>> code?
>>
>> The release pages here say something to the effect of
>>
>> "JBrowse-1.16.3-dev.zip - use this if you modify jbrowse source code or
>> use plugins"
>>
>> Only the -dev version or a github clone of the jbrowse repo will perform
>> the rebuild with the plugins properly
>>
>> Hope that helps.. the whole reason for this is the webpack modernization
>> of our code that got us to where we don't dynamically load plugins but
>> instead bundle them at build time.
>>
>>
>> -Colin
>>
>> On Thu, Feb 28, 2019 at 1:14 PM thomas <
>> tsi...@re...> wrote:
>>
>>> Hello all,
>>>
>>> I am fairly new to Jbrowse. I have installed the latest version
>>> (jbrowse-1.16.3-release) in a docker container (ubuntu xenial) and it
>>> works fine.
>>>
>>> Problems arise when I try to install a plugin. I am trying to install
>>> and use VariantEffectPlugin
>>> (https://github.com/hans-vg/jbplugin-varianteffect).
>>>
>>> I copied the plugin folder into the jbrowse/plugins directory, added the
>>> plugin to jbrowse.conf and ran ./setup.sh again - and get an error
>>> "plugin VariantEffectPlugin not found, please ensure the plugin was
>>> included in this jbrowse unit".
>>>
>>> I tried to add the plugin using many syntaxes in jbrowse.conf:
>>>
>>> in [GENERAL]
>>>
>>> plugins += VariantEffectPlugin
>>>
>>> or
>>>
>>> [plugins.VariantEffectPlugin]
>>> location = plugins/VariantEffectPlugin
>>>
>>> or
>>>
>>> [plugins.VariantEffectPlugin]
>>> location = /var/www/jbrowse/plugins/VariantEffectPlugin
>>>
>>>
>>> The files exists and the plugin folder is open in reading.
>>>
>>>
>>> I cannot seem to figure out what am I doing wrong.
>>>
>>> is jbrowse-1.16.3-release the right version to use with plugins?
>>>
>>> is there something that I'm missing to load the plugins properly?
>>>
>>>
>>> Best regards,
>>>
>>>
>>> Thomas
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>