The following sections should help you install the library on your machine.
Some of the instructions are based on the CellProfiler instructions, the guys behind the javabridge library.
However, if you should encounter problems or if you would like to submit improvements on the instructions below, please use the following mailing list:
https://groups.google.com/forum/#!forum/python-weka-wrapper
You need an Oracle JDK (1.7+) installed and the JAVA_HOME environment variable pointing to the installation directory in order to use python-weka-wrapper3 library.
Why not OpenJDK? Weka is developed and tested with Oracle’s JDK/JRE. There is no guarantee that it will work with OpenJDK.
First, you need to be able to compile C/C++ code and Python modules:
$ sudo apt-get install build-essential python3-dev
Now, you can install the various packages that we require for installing python-weka-wrapper3:
$ sudo apt-get install python3-pip python3-numpy
The following packages are optional, but necessary if you also want some graphical output:
$ sudo apt-get install python3-pil python3-matplotlib python-pygraphviz
Install OpenJDK as well, in order to get all the header files that javabridge compiles against (but don’t use it for starting up JVMs):
$ sudo apt-get install default-jdk
Finally, you can use pip3 to install the Python packages that are not available in the repositories:
$ sudo pip3 install javabridge
$ sudo pip3 install python-weka-wrapper3
First, become the superuser:
$ su
You need to be able to compile C/C++ code and Python modules:
$ apt-get install build-essential python3-dev
Now, you can install the various packages that we require for installing `python-weka-wrapper3:
$ apt-get install python3-pip python3-numpy
The following packages are optional, but necessary if you also want some graphical output:
$ apt-get install python3-imaging python3-matplotlib python-pygraphviz
Download an Oracle JDK and un-tar it in /opt (e.g., /opt/jdk1.7.0_75/). Export the Java home directory as follows (required for the javabridge installation):
$ export JAVA_HOME=/opt/jdk1.7.0_75/
Finally, you can use pip3 to install the Python packages that are not available in the repositories:
$ pip3 install javabridge
$ pip3 install python-weka-wrapper3
Please note, when using python-weka-wrapper3 as a normal user, don’t forget to export the JAVA_HOME environment variable as described above (e.g., add it to your .profile).
Here are some rough instructions (as superuser):
See these general instructions for installing Python on Linux. You need to be able to compile C/C++ code and Python modules (i.e., Python header files are required). By installing OpenJDK, you should be able to compile javabridge against its header files (for JNI access).
Then you need to install the following Python packages, preferably through your package manager (e.g., yum). Please note that on a headless machine, you can omit the packages marked as optional, as they are only required for graphical output and plots:
Once these libraries are installed, you can use pip3 to install the remaining Python packages:
$ sudo pip3 install javabridge
$ sudo pip3 install python-weka-wrapper3
Please follow these general instructions for installing Python.
In order to compile C/C++ code, you need to install Xcode through Apple’s App Store. Once installed you can install the XCode command-line tools by issuing the command xcode-select --install in a terminal.
Also, install graphviz using homebrew (brew install pkg-config and brew install graphviz) for visualizing trees and graphs.
You need to install the following Python packages:
Once these libraries are installed, you can use pip to install the remaining Python packages:
$ pip3 install javabridge
$ pip3 install python-weka-wrapper3
Please note: You need to make sure that the bitness of your environment is consistent. I.e., if you install a 32-bit version of Python, you need to install a 32-bit JDK and 32-bit numpy (or all of them are 64-bit).
Perform the following steps:
- download from here
- install using python get-pip.py
- download numpy 1.9.x MKL (or later) for Python 3.4/3.5 (cp34/cp35) and your bitness (32 or 64 bit)
- install the .whl file using pip: pip install numpy-X.Y.Z.whl
- download javabridge (or later) for Python 3.4/3.5 (cp34/cp35) and your bitness (32 or 64 bit)
- install the .whl file using pip: pip install javabridge-X.Y.Z.whl
If you want to use the plotting functionality, you need to install matplotlib as well:
> pip install python-weka-wrapper
For being able to compile libraries on Windows, you need the Microsoft Build Tools 2015 installed.
You have two options for installing the library from source, either through a release archive or using the bleeding edge source code that is available through the Github repository.
Go to the releases page on Github and download the Source code archive (zip or tar.gz) of the release that you want to install. After the download finishes, decompress the archive. Open a terminal/command prompt and execute the following command from within the directory with the setup.py file:
$ python3 setup.py install
Check out the section on virtualenv as well, if you would rather install it in a disposable location.
Clone the Github repository as follows:
git clone https://github.com/fracpete/python-weka-wrapper3.git
Change into the newly created directory and install the library using the following command:
$ python3 setup.py install
Check out the section on virtualenv as well, if you would rather install it in a disposable location.