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Desktop JBrowse Installation on UNIX Systems

Hierarchical Checkbox Plugin

  1. In destination directory, run
git clone https://github.com/bhofmei/jbplugin-hierarchicalcheckbox HierarchicalCheckboxPlugin
  1. In tracks.conf of datset directory to be opened in Desktop JBrowse, add
[plugins.HierarchicalCheckboxPlugin]
location = full-path-to-plugin/HierarchicalCheckboxPlugin
  1. See plugin repository for usage information.

Methylation Plugin

  1. In destination directory, run
git clone https://github.com/bhofmei/jbplugin-methylation MethylationPlugin
  1. In tracks.conf of datset directory to be opened in Desktop JBrowse, add
[plugins.MethylationPlugin]
location = full-path-to-plugin/MethylationPlugin
isAnimal = false
extendedModifications = false
  1. See plugin repository for additional configuration options and usage information.

Motif Density Plugin

  1. In destination directory, run
git clone https://github.com/bhofmei/jbplugin-motifdens MotifDensityPlugin
  1. In tracks.conf of datset directory to be opened in Desktop JBrowse, add
[plugins.MotifDensityPlugin]
location = full-path-to-plugin/MotifDensityPlugin
  1. See plugin repository for usage information.

Screenshot Plugin

The screenshot plugin DOES NOT work for the desktop version of JBrowse because internet-accessible URLs are necessary to create the screenshot.

Sequence Views Plugins

  1. In destination directory, run
git clone https://github.com/bhofmei/jbplugin-seqview SeqViewsPlugin
  1. In tracks.conf of datset directory to be opened in Desktop JBrowse, add
[plugins.SeqViewsPlugin]
location = full-path-to-plugin/SeqViewsPlugin
  1. See plugin repository for usage information.

Small RNA Plugin

  1. In destination directory, run
git clone https://github.com/bhofmei/jbplugin-smallrna SmallRNAPlugin
  1. In tracks.conf of datset directory to be opened in Desktop JBrowse, add
[plugins.SmallRNAPlugin]
location = full-path-to-plugin/SmallRNAPlugin
isAnimal = false
  1. See plugin repository for additional configuration options and usage information.

Stranded Plot Plugin

  1. In destination directory, run
git clone https://github.com/bhofmei/jbplugin-strandedplot StrandedPlotPlugin
  1. In tracks.conf of datset directory to be opened in Desktop JBrowse, add
[plugins.StrandedPlotPlugin]
location = full-path-to-plugin/StrandedPlotPlugin
  1. See plugin repository for usage information.

Track Scores Plugin

  1. In destination directory, run
git clone https://github.com/bhofmei/jbplugin-trackscores TrackScorePlugin
  1. In tracks.conf of datset directory to be opened in Desktop JBrowse, add
[plugins.TrackScorePlugin]
location = full-path-to-plugin/TrackScorePlugin
  1. See plugin repository for usage information.

Wiggle SVG Plot Plugin

This plugin will work for Desktop JBrowse, but is not recommended to be used. The primary goal of the Wiggle SVG Plot Plugin is for screenshots with the Screenshot Plugin and the Screenshot Plugin does not work for Desktop JBrowse.

Y-Scale Menu Plugin

  1. In destination directory, run
git clone https://github.com/bhofmei/jbplugin-yscale YScaleMenuPlugin
  1. In tracks.conf of datset directory to be opened in Desktop JBrowse, add
[plugins.YScaleMenuPlugin]
location = full-path-to-plugin/YScaleMenuPlugin
  1. See plugin repository for usage information.