Linux install guide for 1.6.x with PyQt5 (Debian based)

Prerequisites

• get a github account
• install and configure git

sudo apt-get install git
git config --global user.name "Your Name"
git config --global user.email [email protected]

• generate and add your ssh key (if ssh key not registered at github, this will lead to error messages with using git later)

ssh-keygen -t dsa -C [email protected]`
cat ~/.ssh/id_dsa.pub

• copy&paste the output and add it as ssh key on github (personel account settings)
• install cmake

sudo apt-get install cmake

Installing dependencies

sudo apt-get install python-h5py python-scipy python-qt5 \ 
python-matplotlib python-drmaa python-pyamf python-qt5-dev \
pyqt5-dev-tools libhdf5-serial-dev python-sklearn \
python-pandas ipython python-setuptools python-pip

Note, that on Ubuntu >= 14 the package python-pyamf is no longer available, but you can download a .deb package from the web

Note, that if you also have a Qt4 installation, you might need to modify /usr/lib/x86_64-linux-gnu/qt-default/qtchooser/default.conf to link it to qt5 rather than qt4

VIGRA (>=1.8.0)

sudo apt-get build-dep python-vigra
git clone https://github.com/ukoethe/vigra.git
cd vigra
mkdir build
cd build
cmake ..
make
sudo make install

You may extend the LD_LIBRARY_PATH according to your installation prefix (e.g. /usr/local/lib) in your .bashrc or use ldconfig to setup the path similarly. Or set it manually by e.g.

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:"/usr/local/lib"

qimage2ndarray

git clone https://github.com/hmeine/qimage2ndarray.git
cd qimage2ndarray
python setup.py build
sudo python setup.py install

libsvm 2.89

wget http://www.csie.ntu.edu.tw/~cjlin/libsvm/oldfiles/libsvm-2.89.zip
unzip libsvm-2.89.zip
cd libsvm-2.89/python
python setup.py build
sudo python setup.py install

rdflib and ontospy

pip install rdflib
pip install ontospy==1.0.0b2

CellCognition

git clone https://github.com/CellCognition/cecog.git
cd cecog
git submodule init
git submodule update

A source tarball including the battery package will be made available soon.

• edit paths to libraries in setup.cfg for instance

include_dirs=/usr/local/include/
library_dirs=/usr/local/lib/

• then execute

python setup.py build

• Local installation into <install_path>

python setup.py install --prefix=<install_path>
PYTHONPATH=$PYTHONPATH:<install_path>/lib/python<version>/site-packages/ CecogAnalyzer.py

or add <install_path>/lib/python/site-packages/ permanently to your environment

• System installation

sudo python setup.py install
CecogAnalyzer.py