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bhofmei / jbplugin-nucdens

No longer actively developed...See README
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Great plugin! minor issue with symlinks that are missing #2

Closed thomasvangurp closed 7 years ago

thomasvangurp commented 7 years ago

Dear Brigitte,

The plugin works great. It does not work out of the box though, I had to make 2 symlinks:

  1. Make a symlink called NucleotideDensityPlugin ln -s jbplugin-nucdens NucleotideDensityPlugin
  2. Inside plugins/NucleotideDensityPlugin make a symlink to View: ln -s js/View/

Cheers, Thomas

bhofmei commented 7 years ago

It seems you did not install the repository as is suggested by the README.

When calling git clone, there's an optional parameter for the new file name. When not included, it defaults to the repository name. Instead of making the symlink, you could

  1. rename the jbplugin-nucdens folder to NucleotideDensityPlugin
  2. reclone the repository using git clone https://github.com/bhofmei/jbplugin-nucdens.git NucleotideDensityPlugin as specified in the README or
  3. change the location of the plugin in jbrowse.conf to location = plugins/jbplugin-nucdens

I'm guessing the symlink for js/View was necessary due to the installation problem mentioned above. If you ran into this error when creating the nucleotide density track, another way around this is to use "type":"NucDensity" instead of "type": "NucleotideDensityPlugin/View/Track/NucleotideDensity" in the track configuration.