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Web Browser JBrowse Installation on UNIX Systems

Hierarchical Checkbox Plugin

  1. In the JBrowse plugins folder, run
git clone https://github.com/bhofmei/jbplugin-hierarchicalcheckbox HierarchicalCheckboxPlugin
  1. In jbrowse.conf (all datatsets can use it) or tracks.conf (specific dataset uses it), add
[plugins.HierarchicalCheckboxPlugin]
location = plugins/HierarchicalCheckboxPlugin
  1. See plugin repository for usage information.

Methylation Plugin

  1. In the JBrowse plugins folder, run
git clone https://github.com/bhofmei/jbplugin-methylation MethylationPlugin
  1. In jbrowse.conf (all datatsets can use it) or tracks.conf (specific dataset uses it), add
[plugins.MethylationPlugin]
location = plugins/MethylationPlugin
isAnimal = false
extendedModifications = false

While plugin declaration should not be included in both jbrowse.conf and tracks.conf, configuration options can be changed.

For example, if most data sets don't need extended modifications, include in jbrowse.conf

[plugins.MethylationPlugin]
location = plugins/MethylationPlugin
extendedModifications = false

For the data which does need extended modifications, include in tracks.conf

[plugins.MethylationPlugin]
extendedModifications = true
  1. See plugin repository for additional configuration options and usage information.

Motif Density Plugin

  1. In the JBrowse plugins folder, run
git clone https://github.com/bhofmei/jbplugin-motifdens MotifDensityPlugin
  1. In jbrowse.conf (all datatsets can use it) or tracks.conf (specific dataset uses it), add
[plugins.MotifDensityPlugin]
location = plugins/MotifDensityPlugin
  1. See plugin repository for usage information.

Screenshot Plugin

  1. In the JBrowse plugins folder, run
git clone https://github.com/bhofmei/jbplugin-screenshot ScreenShotPlugin
  1. In jbrowse.conf (all datatsets can use it) or tracks.conf (specific dataset uses it), add
[plugins.ScreenShotPlugin]
location = plugins/ScreenShotPlugin
apiKey = <optional_api_key>
htmlFeatures = false
  1. See plugin repository for additional configuration options and usage information.

Sequence Views Plugins

  1. In the JBrowse plugins folder, run
git clone https://github.com/bhofmei/jbplugin-seqview SeqViewsPlugin
  1. In jbrowse.conf (all datatsets can use it) or tracks.conf (specific dataset uses it), add
[plugins.SeqViewsPlugin]
location = plugins/SeqViewsPlugin
  1. See plugin repository for usage information.

Small RNA Plugin

  1. In the JBrowse plugins folder, run
git clone https://github.com/bhofmei/jbplugin-smallrna SmallRNAPlugin
  1. In jbrowse.conf (all datatsets can use it) or tracks.conf (specific dataset uses it), add
[plugins.SmallRNAPlugin]
location = plugins/SmallRNAPlugin
isAnimal = false
  1. See plugin repository for additional configuration options and usage information.

Stranded Plot Plugin

  1. In the JBrowse plugins folder, run
git clone https://github.com/bhofmei/jbplugin-strandedplot StrandedPlotPlugin
  1. In jbrowse.conf (all datatsets can use it) or tracks.conf (specific dataset uses it), add
[plugins.StrandedPlotPlugin]
location = plugins/StrandedPlotPlugin
  1. See plugin repository for usage information.

Track Scores Plugin

  1. In the JBrowse plugins folder, run
git clone https://github.com/bhofmei/jbplugin-trackscores TrackScorePlugin
  1. In jbrowse.conf (all datatsets can use it) or tracks.conf (specific dataset uses it), add
[plugins.TrackScorePlugin]
location = plugins/TrackScorePlugin
  1. See plugin repository for usage information.

Wiggle SVG Plot Plugin

  1. In the JBrowse plugins folder, run
git clone https://github.com/bhofmei/jbplugin-wigglesvg WiggleSVGPlotPlugin
  1. In jbrowse.conf (all datatsets can use it) or tracks.conf (specific dataset uses it), add
[plugins.WiggleSVGPlotPlugin]
location = plugins/WiggleSVGPlotPlugin
  1. See plugin repository for usage information.

Y-Scale Menu Plugin

  1. In the JBrowse plugins folder, run
git clone https://github.com/bhofmei/jbplugin-yscale YScaleMenuPlugin
  1. In jbrowse.conf (all datatsets can use it) or tracks.conf (specific dataset uses it), add
[plugins.YScaleMenuPlugin]
location = plugins/YScaleMenuPlugin
  1. See plugin repository for usage information.