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adding plugin hosed jbrowse #1025

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malcook opened this Issue Mar 16, 2018 · 7 comments

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@malcook

malcook commented Mar 16, 2018

Hello,

JBrowse 1.13.0 installed last night from a fork of master worked great.

Until....

I tried installing an Plugin and found that JBrowse would get hang on "Loading..."

The extension was: Sequence Motif Density Plugin created by @bhofmei

After following her installation instructions, JBrowse could not find the plugin I registered in the config files (I tried both .text and .json). I figured her instructions lacked the directions to re-run setup.sh, so I did and restarted the server.

It was at this point that I'm hanging on "Loading...".

My only success in backing out of this was reinstalling JBrowse completely.

I notice a few commits today having to do with plugins, so, perhaps this is a know issue now fixed in head?

All advice appreciated (included better recovery strategy than complete reinstallation).

Cheers!

@cmdcolin

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cmdcolin commented Mar 16, 2018

I think the problem is that domReady was specified in the middle of the dependencies list. There is special new code in the plugin loader to make domReady an unused dependency, but since it was in the middle, it was not filtered out properly. @bhofmei, do you want to remove domReady as dependency? It should cause no problem

@cmdcolin

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cmdcolin commented Mar 16, 2018

Specifically in the file js/View/Dialog/MotifDensityDialog.js

@rbuels

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rbuels commented Mar 18, 2018

oh i need to patch that loader

@rbuels rbuels added this to the 1.13.1 milestone Mar 18, 2018

@rbuels rbuels added the bug label Mar 18, 2018

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rbuels commented Mar 18, 2018

@malcook you re-ran ./setup.sh after installing her plugin right?

@rbuels rbuels added user support and removed bug labels Mar 20, 2018

@rbuels rbuels closed this in 1acaa3a Mar 23, 2018

@malcook

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malcook commented Mar 23, 2018

@rbuels - thanks for asking - yes I had re-run ./setup.sh

Alas, @bhofmei, now when I try with the latest plugin on top of fresh jbrowse clone from yesterday it interferes with the "Available Tracks" panel, which appears blank. They re-appear if I comment out jbrowse.conf as follows:

# [plugins.MotifDensityPlugin]
# location = plugins/MotifDensityPlugin

and restart jbrowse

> utils/jb_run.js 

BTW - they include most happily for me a MultiBigWig displaying various signals over yeast protein, e.g.:

image

@bhofmei

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bhofmei commented Mar 23, 2018

@rbuels

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rbuels commented Mar 23, 2018

@malcook @bhofmei can we move this discussion to bhofmei/jbplugin-motifdens#2?

@malcook I can try to help out over there since @bhofmei is indisposed

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