Bio7 2.4 for Linux Released

July 5, 2016
By

(This article was first published on R, and kindly contributed to R-bloggers)

04.07.2016

A new Bio7 Linux release is available at http://bio7.org. The general release note for Bio7 2.4 can be found here!

linuxscreen1

Installation:

Bio7 for Linux comes bundled with the latest Java Runtime Environment.

To use R with Bio7 you have to install R for Linux.

In addition you have to install Rserve configured to use ‘cooperative mode’ (shared workspace in Rserve and R mode) which can be downloaded here:

https://bitbucket.org/maustenfeld/bio7-new/downloads

In the R prompt type the following command to install the compiled package (replace with your file path!):

install.packages(“Users/yourName/Downloads/Rserve_1.8-4_Linux_cooperative.tar.gz”, repos=NULL)

You can also compile Rserve by yourself. For an HowTo please consult the Bio7 documentation here.

Miscellaneous:

Added a tiny script to install useful default R packages for Bio7 to use all available GUI functionalities (e.g. rmarkdown, rgdal, spatstat, formatR, knitr, etc.). To install the packages start Rserve and execute the action Scripts->RScripts->Install_R_Packages in the Bio7 main menu. Please note that this only works if all dependencies for the packages are installed for compilation.

Troubleshooting Layout:

Linux comes in different flavours and it might be that you have to correct the Bio7 GTK *.css file for a little improved layout. If you see an artefact like this (‘Maximize’ button) just increase the size of the *.css toolbar variables.

linuxscreen4

The default CSS file can be found here:

/Bio7/plugins/com.eco.bio7.themes_2.0.0.201607050754/css/e4_default_gtk.css

The following changed css attributes will correct the height of the toolbars (changed attributes are bold):

.MPartStack {
……………………………………
color: ‘#org-eclipse-ui-workbench-INACTIVE_TAB_TEXT_COLOR’;
 swt-tab-height: 36.0px;

}

.MPartStack.active {
…………………………………..
swt-shadow-visible: false;
 swt-tab-height: 36.0px;
}

/*Important to set height for the view menus!*/
CTabFolder {
swt-corner-radius: 15.0;
swt-tab-height: 36.0px;
}

Of course you can change other attributes as well, e.g.,  if you want to change a color, etc. If you have good suggestions let me know.

Screenshots:

linuxscreen2

linuxscreen3

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