Bio7 2.0 for Linux Released!

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).

 

 

 

 

 

 

 

3 thoughts on “Bio7 2.0 for Linux Released!

  1. admin

    Hello,

    please note that a standard installation of R is needed.
    If Revolution R is a standard installation of R it should work.

    R is expected in the OS Linux path:
    /usr/lib/R

    you can change the path in the Bio7 preferences, see:
    http://bio7.org/manual/Main.html#toc-Section-6.1

    Rserve is expected under
    /usr/lib/R/site-library
    adjustable in the preferences, see:

    http://bio7.org/manual/Main.html#toc-Subsubsection-4.7.2.11

    Rserve hast be compiled and installed with the shell command:

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

    to that location.

    I hope this info helps.

  2. admin

    Ok. I installed CentOS 7 and Bio7 on a Virtual Maschine.
    CentOS fails to use GTK 3 with Eclipse.

    If Bio7 hangs at startup please add the following argument to the Bio7.ini file in the Bio7 installation folder:

    –launcher.GTK_version
    2

    This arg had to be added like this in the*.ini file:
    ............................................
    plugins/
    org.eclipse.equinox.launcher.gtk.linux...........
    --launcher.GTK_version
    2
    ..................

    After that Bio7 should be started on CentOS!

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