Plugins not starting properly ?

colindaven commented 8 years ago

Hi,

nice ideas on these plugins.

Trying them out in a dev version, I haven't got them going reliably yet.

git clone into plugins

Result: JBrowse_test$ ls -1 plugins/ RegexSequenceSearch gccontent sashimiplot

2. jbrowse.conf

uncomment and edit the example below to enable one or more

JBrowse plugins

[ plugins.gccontent ] location = plugins/gccontent [ plugins.sashimiplot ] location = plugins/sashimiplot

3. data/trackList.json stanzas:

    {
      "storeClass" : "JBrowse/Store/SeqFeature/IndexedFasta",
      "type": "GCContent/View/Track/GCContentXY",
      "label": "GCContent",
      "urlTemplate" : "../SBKv2con.fa",
      "bicolor_pivot": 0.5
    },
    {
  "label": "star_sashimi_junctions",
  "storeClass": "JBrowse/Store/SeqFeature/BAM",
  "type": "SashimiPlot/View/Track/Sashimi",
  "urlTemplate": "tracks/STAR1Aligned.out_s.bam",
    "chunkSizeLimit": 50000000,
    "key" : "tEST sashimi",
    "useXS": true
    }

Output on clicking track - nothing - I would expect a "datafile not found" message or similar if the BAM or FASTA are not being found. Am I missing something here?

Thanks! Colin

cmdcolin commented 8 years ago

Sorry was out on vacation last week

I should probably expand on the "how to install" section

Generally this looks exactly right, except I would use

[ plugins.GCContent ]
location = plugins/gccontent

The name of the plugin is officially "GCContent" instead of gccontent, and some of the paths depend on that inside the code :)

Alternatively, and I guess this demonstrates how there are many ways to include the plugin, you can just name the folder plugins/GCContent and plugins/SashimiPlot in the first place, and then just say this in your jbrowse.conf

plugins += GCContent
plugins += SashimiPlot

Equivalently, in the jbrowse_conf.json, that would mean just having

"plugins": ["GCContent", "SashimiPlot"]

So it is essentailly just an array of folder names to look for in the plugins directory

Similarly, the .conf format representation as

[ plugins.GCContent ]
location = plugins/gccontent

Would be equivalent to this in the json format

"plugins": [{
"name": "GCContent",
"location": "plugins/gccontent"
}]

This is similar, but it is an array of objects with the plugin name and location.

This is actually such a nuanced type of thing (especially considering the different .conf and json representations) that I will add it to the new JBrowse FAQ :)

cmdcolin commented 8 years ago

See http://gmod.org/wiki/JBrowse_FAQ#How_do_I_install_a_plugin

Let me know if there are any other issues!

colindaven commented 8 years ago

Hi, thanks Colin, very much appreciated. The plugins look great.

Perhaps you can add the following example SequenceChunks to the gccontent github example. I couldn't get the IndexedFasta to work but would vastly prefer to use the already imported SequenceChunks anyway and many others might prefer this too (I missed the fact you could use SequenceChunks on my first attempt.

    {
      "storeClass" : "JBrowse/Store/SeqFeature/SequenceChunks",
      "type": "GCContent/View/Track/GCContentXY",
      "label": "GCContentXY",
      "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
      "bicolor_pivot": 0.5
    },

Cheers, colin

elsiklab / gccontent

Plugins not starting properly ? #2

uncomment and edit the example below to enable one or more

JBrowse plugins