Bio7 2.0 for Linux Released!

January 31, 2015
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(This article was first published on » R, and kindly contributed to R-bloggers)

01.02.2015

I released the Linux version of Bio7 2.0 (see screenshot below).

screenlinux

For an overview of the new Bio7 features follow the link: Bio7 2.0 new features

Added Linux features:

  • A new Java menu action (in the Scripts menu) is available to start a Py4J server which can communicate to Java and CPython (if enabled in the native preferences of Bio7 and Py4J is installed in the local Python distribution). With this feature it is, e.g., possible to transfer ImageJ values to CPython or call the Bio7 Java API.
  • Improved the embedded native pseudo terminal to send signals to a process tree (e.g., SIGINT = STRG+C).
  • Added an option in the native preferences to interpret a Python script with a a native CPython interpreter >=3.0.

Installation:

Download Bio7 and simply unzip the Bio7 archive file in your preferred location. Bio7 comes bundled with a JRE so you don’t need to install Java separately. The Bio7 application was tested on Ubuntu 14.04 (minimum requirement).

R features:

For the Linux version of Bio7 2.0 R and Rserve have to be installed. For the use in Bio7 Rserve has to be compiled with a special flag to enable the cooperative mode (see below).

In a shell simply execute:

sudo PKG_CPPFLAGS=-DCOOPERATIVE R CMD INSTALL Rserve_1.8-1.tar.gz

The command will compile and install the Rserve package in your default Linux R application. This is necessary to share the R workspace when you switch from a local Rserve connection to the native Bio7 R console (see this video for an explanation of the new connection mode in Bio7).

Please note that the default R package location of Bio7 is: /usr/lib/R/site-library

The location (and the path to R) can be changed in the R preferences of Bio7 (e.g., menu: R->Preferences).

 

 

 

 

 

 

 

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