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(This article was first published on <strong><a href="http://bio7.org/?p=2974"> R – Bio7 Website</a></strong>, and kindly contributed to <a rel="nofollow" href="https://www.r-bloggers.com/">R-bloggers)</a> </div>
<p><strong>20.10.2017</strong></p>
<p>Beside a massive of amount of R packages and <a rel="nofollow" href="https://imagej.nih.gov/ij/plugins/" target="_blank">ImageJ plugins</a> Bio7 can be extended with Eclipse plugins useful for data science and programming.</p>
<p>Some of them could also be very useful for R related developments (e.g., to develop R packages or distribute Shiny apps).</p>
<h2>Installation of Eclipse Plugins</h2>
<p>One  way to install Eclipse plugins is by using the <a rel="nofollow" href="https://wiki.eclipse.org/FAQ_What_is_the_Update_Manager%3F" target="_blank">Update Manager</a> in the help menu (<strong>Help->Install New Software</strong>).</p>
<p>Thus the first step to install a plugin is to open the Update Manager and selecting the category “<strong>Eclipse Repository – http://download.eclipse.org/releases/neon</strong>” (see screenshot below!)</p>
<p><img sizes="(max-width: 419px) 100vw, 419px" src="https://i1.wp.com/bio7.org/wp-content/uploads/2017/10/updatemanager.jpg?resize=419%2C336" alt="" class="wp-image-2983" data-recalc-dims="1"></p>
<p>Another handy way of searching and installing Eclipse plugins is by using the <a rel="nofollow" href="https://www.eclipse.org/mpc/" target="_blank">Marketplace Client</a> plugin which must be installed firstly with the Update Manager.</p>
<p>Search for the Marketplace Client (e.g., “marketplace”) plugin to filter, select and install the <a rel="nofollow" href="https://www.eclipse.org/mpc/" target="_blank">Marketplace Client</a>.</p>
<p>The following plugins can be installed using either the Marketplace Client or the Update Manager.</p>
<h2>Database Remote Files and Shells</h2>
<p><strong>EGit<br>
</strong><br>
<a rel="nofollow" href="https://marketplace.eclipse.org/content/egit-git-team-provider" target="_blank">https://marketplace.eclipse.org/content/egit-git-team-provider<br>
</a>The powerful Eclipse Git plugin to connect Bio7 with Git repositories.</p>
<p><strong>TM-Terminal<br>
</strong><br>
<a rel="nofollow" href="http://marketplace.eclipse.org/content/tcf-terminals" target="_blank">http://marketplace.eclipse.org/content/tcf-terminals </a><br>
A true native terminal with SSH,Telnet and Serial line support. Bio7 comes already with a pseudo-terminal but lacks the support of a <a rel="nofollow" href="https://en.wikipedia.org/wiki/Pseudoterminal" target="_blank">pty </a>connection and <a rel="nofollow" href="https://en.wikipedia.org/wiki/ANSI_escape_code" target="_blank">ANSI escape sequences</a> (but can be controlled from a Bio7 API interface). The terminal can also be installed with the Update-manager searching for “tm” (see screenshot below).</p>
<p><img sizes="(max-width: 419px) 100vw, 419px" src="https://i1.wp.com/bio7.org/wp-content/uploads/2017/10/tmterminalupdatemanager.jpg?resize=419%2C350" alt="" class="wp-image-2986" data-recalc-dims="1"></p>
<p><strong>Remote System Explorer</strong></p>
<p><a rel="nofollow" href="https://marketplace.eclipse.org/content/remote-system-explorer-ssh-telnet-ftp-and-dstore-protocols" target="_blank">https://marketplace.eclipse.org/content/remote-system-explorer-ssh-telnet-ftp-and-dstore-protocols<br>
</a>A plugin to connect Bio7 with SSH, Telnet, FTP and DStore protocols.This plugin work very well with a remote connection and makes it easy to transfer data from a local workspace to a remote server. Remote files can be opened, edited and stored with the available Bio7 editors (e.g., a *.html file with the JavaFX editor – see screenshot below).<br>
Apropos, please use an OpenSSH key for, e.g. a SFTPconnection!). It works great together with the TM-Terminal plugin.</p>
<p><img sizes="(max-width: 1917px) 100vw, 1917px" src="https://i1.wp.com/bio7.org/wp-content/uploads/2017/10/remotesystemsexpl.png?w=450" alt="" class="wp-image-2987" data-recalc-dims="1"></p>
<p><strong>DBWeaver<br>
</strong><br>
<a rel="nofollow" href="https://marketplace.eclipse.org/content/dbeaver" target="_blank">https://marketplace.eclipse.org/content/dbeaver<br>
</a>“DBeaver is free universal SQL client/database tool for developers and database administrators. It can work with any database server which has JDBC driver.” (source: website DBWeaver)<br>
DBWeaver is a great database tool and plugin for Eclipse and can also be installed into Bio7 to control and edit R database connections.<br>
<strong><br>
</strong></p>
<h2>Scripting Editors with Bio7 interpret support</h2>
<p>The following three editors can be used within the current Bio7 process to execute scripts using the Bio7 interface. It is important however to create a language project first to profit from the advanced editor features.</p>
<p>Bio7 will recognize the opened editor type and interpret the current opened script with the embedded script interpreter of Bio7 when using the dedicated toolbar action.</p>
<p>Please use the context menu action “Open with” to open the scripts with the installed editors instead of the default Bio7 editors (Groovy, Jython/Python editors are available by default in Bio7).</p>
<p><a rel="nofollow" href="https://youtu.be/v9TFfw3bv9g" target="_blank">Here a video installing and using the JavaScript editor</a> as an general example.</p>
<p><strong>JSDT<br>
</strong><br>
<a rel="nofollow" href="https://eclipse.org/webtools/jsdt/" target="_blank">https://eclipse.org/webtools/jsdt/<br>
</a>JavaScript editor and development tools. Install with the Update-manager (search for JavaScript – see video above).</p>
<p><strong>PyDev Editor<br>
</strong><br>
<a rel="nofollow" href="https://marketplace.eclipse.org/content/pydev-python-ide-eclipse" target="_blank">https://marketplace.eclipse.org/content/pydev-python-ide-eclipse</a><br>
A very powerful Python editor which can be used to execute Bio7 Jython and Python scripts instead of the Bio7 default editor.<br>
In addition Bio7 can use the PyDev editor to execute scripts running on the Bio7 Java classpath. If you open Jython/Python scripts with the PyDev editor the default Bio7 action will be visible to execute the scripts on the Bio7 classpath.</p>
<p><strong>Groovy Editor</strong></p>
<p><a rel="nofollow" href="https://github.com/groovy/groovy-eclipse/wiki" target="_blank">https://github.com/groovy/groovy-eclipse/wiki</a><br>
(Add site: http://dist.springsource.org/snapshot/GRECLIPSE/e4.7/ to the Update Manager) <a rel="nofollow" href="http://dist.springsource.org/snapshot/GRECLIPSE/e4.7/" target="_blank"><br>
</a>A more powerful Groovy editor. Can also be used with the Bio7 classpath if scripts are opened with this editor instead.</p>
<h2>General programming editors and extensions</h2>
<p><strong>Eclipse CDT<br>
</strong><br>
<a rel="nofollow" href="https://marketplace.eclipse.org/content/eclipse-cdt-cc-development-tooling" target="_blank">https://marketplace.eclipse.org/content/eclipse-cdt-cc-development-tooling<br>
</a>Powerful C/C++ editor and development tooling.</p>
<p><strong>Arduino C++ IDE:<br>
</strong><br>
<a rel="nofollow" href="https://marketplace.eclipse.org/content/arduino-c-ide" target="_blank">https://marketplace.eclipse.org/content/arduino-c-ide</a><br>
A great Arduino extension of the C++ editor of Eclipse.<a rel="nofollow" href="https://www.youtube.com/watch?v=TtPvkPpAx0E" target="_blank"> See this video for an introduction</a>. Bio7 embedds some Java libs to communicate with an Arduino (<a rel="nofollow" href="https://github.com/Bio7/bio7_examples/tree/master/Bio7_Java_Examples/src/arduino" target="_blank">see Bio7 examples</a>).</p>
<p><strong>Photran (comes with PTP)</strong></p>
<p><a rel="nofollow" href="https://eclipse.org/ptp/" target="_blank">https://eclipse.org/ptp/</a><br>
<a rel="nofollow" href="http://www.eclipse.org/photran/" target="_blank">http://www.eclipse.org/photran/<br>
</a>An Integrated Development Environment and Refactoring Tool for Fortran</p>
<p><strong>Julia Editor<br>
</strong><br>
<a rel="nofollow" href="https://github.com/JuliaComputing/JuliaDT" target="_blank">https://github.com/JuliaComputing/JuliaDT</a><br>
A Julia editor in an early stage. But very promising.</p>
<p><strong>Bash Editor</strong></p>
<p><a rel="nofollow" href="https://marketplace.eclipse.org/content/bash-editor" target="_blank">https://marketplace.eclipse.org/content/bash-editor</a><br>
A bash editor for bash scripts. Perfect for the use with the above linked TM-Terminal and Remote Systems Explorer.</p>
<p><strong>Jeeeyul’s Eclipse Themes</strong></p>
<p><a rel="nofollow" href="https://marketplace.eclipse.org/content/jeeeyuls-eclipse-themes" target="_blank">https://marketplace.eclipse.org/content/jeeeyuls-eclipse-themes</a><br>
To install more themes into Bio7.</p>
<p><strong>pde-tools</strong></p>
<p><a rel="nofollow" href="https://github.com/jeeeyul/pde-tools#crazy-outline" target="_blank">https://github.com/jeeeyul/pde-tools#crazy-outline<br>
</a>A plugin which adds clipboard history support and a crazy outline view.</p>
<p><strong>WindowBuilder</strong></p>
<p><a rel="nofollow" href="https://marketplace.eclipse.org/content/windowbuilder" target="_blank">https://marketplace.eclipse.org/content/windowbuilder<br>
</a>A very powerful builder for Graphical User Interfaces for SWT, etc.<br>
In Bio7 a wizard is available to create a template for the builder (File->New->Bio7 Java Projects->Bio7 Java Project (WindowBuilder template)).<br>
You can then open this template with the WindowBuilder to create interfaces (e.g., to create R interfaces using the new Bio7 R API). The created interface can be compiled dynamically with Bio7 (compiling the main class) and executed instantly in the current Bio7 process (see screenshot below)</p>
<p><img sizes="(max-width: 1919px) 100vw, 1919px" src="https://i1.wp.com/bio7.org/wp-content/uploads/2017/10/windowbuilder.png?w=450" alt="" class="wp-image-2988" data-recalc-dims="1"></p>
<p>More plugins can be found with the Eclipse Marketplace Client. It depends however how useful the plugins are in the context of Bio7.</p>
<p> </p>
<p> </p>
<p> </p>
	<p>
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