Brigitte Hofmeister's JBrowse Plugins

All JBrowse plugins created by Brigitte Hofmeister

To see all the plugins in action, go to https://bhofmei.github.io/bhofmei-jbplugins/.

Contents

• Epigenomics Visualization
  • DNA Methylation Plugin: Visualize bp-resolution methylation levels colored by sequence context
  • Small RNA Plugin: Visualize small RNA alignments colored by size and stranded y-axis positioning
  • Stranded Plot Plugin: Visualize plus and minus strand coverage in a single track simulataneously
• Additional Features
  • Hierarchical Checkbox Plugin: "Select all" (or deselect all) tracks of a category in the hierarchical track list
  • Motif Density Plugin: Density map of user-specified sequence motifs and multiple color configuration options
  • Screenshot Plugin: Makes taking screenshots easy with PhantomJS
  • Wiggle SVG Plot Plugin: SVG-based track type for wiggle plots; most useful for screenshots
• User Experience
  • Sequence Views Plugins: Force feature or histogram views
  • Track Scores Plugin: Adds a track menu item to change between autoscale types and manual limits
  • Y-Scale Plugin: Adds global menu option to set the y-scale position of all visible tracks

Citation

If these plugins are used for research or publication, please cite the following. I've spent a lot of time on these and would appreciate the recognition.

Enhanced JBrowse plugins for epigenomics data visualization Brigitte T. Hofmeister, Robert J. Schmitz BMC Bioinformatics 19(159); doi: 10.1186/s12859-018-2160-z

You can read the original article at BMC Bioinformatics.

JBrowse Versions

These plugins are designed for JBrowse v1.11.6 - v1.12.6. Installation directions are for these versions.

JBrowse v1.13.0+ uses a radically different system to download dependencies and build the site. The plugins are likely to work as-is but have not been tested extensively. See the JBrowse documentation for more information.

Installation for Unix Systems

For Web-Browser-Based JBrowse

Bulk installation

1. Add this repositiory to the plugin folder of JBrowse, i.e. jbrowse-root/plugins/.

git clone https://github.com/bhofmei/bhofmei-jbplugins BhofmeiPlugins

2. Update plugins.json to install the plugins you are interested in

• Default is to install all
• Set to false for plugins not to install

3. Run install.sh

• Assumes that this script is located at jbrowse-root/plugins/BhofmeiPlugins
• Use -p prefix to specify the install directory if this script is located elsewhere
• See install.sh -h for additional parameters

4. Copy the output to jbrowse.conf or a dataset tracks.conf as applicable

• If you prefer to use the JSON specification for jbrowse_conf.json or trackList.json, run as install.sh -j

5. See the indivual plugin repositiories for plugin-specific configuration options

Individual plugin installation

See browser-unix-install.md.

For Desktop-Based JBrowse

Bulk installation

1. Install this repository in desired directory

git clone https://github.com/bhofmei/bhofmei-jbplugins BhofmeiPlugins

2. Update plugins.json to install the plugins you are interested in

• Default is to install all
• Set to false for plugins not to install

3. Run install.sh -d -p <prefix>

• Use -p <prefix> to specify the directory to install the plugins. The default is ../
• When prefix is a relative path, it resolves the path and uses the absolute path for the output config

4. Copy the output to tracks.conf for the dataset directory to be opened

• If you prefer the JSON specification, run with the -j option and copy output to trackList.json

5. See the indivual plugin repositiories for plugin-specific configuration options

Individual plugin installation

See desktop-unix-install.md.

Installation for Windows Systems Desktop-Based JBrowse

See windows desktop installation for steps to download plugins of interest.

Updating for Unix Systems

Bulk updating

1. In plugins.json, specify which plugins to update

• Use true to update
• Use false if not installed or don't want updated

2. Run update.sh

• By default, looks for plugins at ../. If they are installed elsewhere, you -p <prefix> where <prefix> is the aboslute or relative path to the directory where all plugins are installed.
• Run update.sh -h to see the other options

Individual plugin updating

To update a single plugin, run git pull within the plugin directory

Updating for Windows Systems

Plugin must be reinstalled; see windows installation and replace the existing plugin.

Testing

Many of the individual plugins have their own unit tests and test data sets.

Additionally, manual integration testing has been done with BrowserStack to verify compatibility with different web browsers and versions.

Fine Print

All plugins are distributed under the Apache License, Version 2.0.