Install Eclipse, R, ImageJ Plugins or Packages in Bio7

18.03.2012

Bio7 can be extended in several different ways with Eclipse plugins, R packages, ImageJ plugins and custom scripts (scripts to extend a menu or executed at startup).

1. To install (suitable) Eclipse plugins the Update-Manager can be used to install plugins from a remote website. An How-To was already posted with the GIT plugin as an example, see: http://bio7.org/?p=1066

2. R packages can be added in two different ways. One way is to use the package installer GUI of Bio7:
http://www.uni-bielefeld.de/biologie/Oekosystembiologie/bio7app/flashtut/rpackagesinstall.htm
Additionally the command line in R can be used to install packages.

3. ImageJ plugins (*.class or *.jar files) have to be installed in the plugins folder of the ImageJ Eclipse plugin which is e.g.: Bio7/plugins/com.eco.bio7.image_1.45.1/plugins.
Note: In the ImageJ Eclipse plugin the typical ImageJ folder structure can be found!

4. Groovy, BeanShell and R scripts, as well as ImageJ macros can be dropped to special folders to extend the default Bio7 menu (startup) functionality. The folders which are scanned by default are:

Path to folders: Bio7/plugins/com.eco.bio7_1.5.0/

Folder Default (see Preferences!)
Script Type Menu Bio7 Component
export_scripts BeanShell,Groovy File->Export-Scripts Main Menu
import_scripts BeanShell,Groovy File->Import-Scripts Main Menu
image_scripts ImageJ Macros Scripts->ImageJ-Macros Main Menu
scripts BeanShell,Groovy Scripts->General-Scripts Main Menu
r_scripts R scripts Scripts->R-Scripts Main Menu
spatial_scripts BeanShell,Groovy Scripts->Spatial-Scripts Main Menu
grid_scripts BeanShell,Groovy Scripts Table View Menu
startup_scripts BeanShell,Groovy Scripts executed at startup if folder available!  –

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