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Installation on Linux
If you use git, clone the repository:
git clone https://github.com/jniediek/combinato.git
If you do not use git, download Combinato from https://github.com/jniediek/combinato/archive/master.zip.
It is possible to skip this step and come back in case of dependcy problems.
Combinato depends on scipy, pywt, matplotlib, pytables, and pyqt. Most modern Linux distributions have these packages installed by default. If you miss any of these packages, use your distribution's package manager to install them.
For example, in Ubuntu and Debian
sudo apt-get install python-scipy python-matplotlib python-pywt python-tables python-qt4
installs all dependencies.
Combinato uses a compiled executable file as backend for clustering. To automatically select the correct file for your operating system, navigate your shell to the Combinato repository and run
python setup_options.py.
Combinato is organized as a collection of executable scripts. These are the files named css-* in the repository's main folder. To be able to execute these scripts, add the repository's folder to your $PATH as shown below.
For some of the tools in the subdirectories signalviewer and tools, it is necessary to add the repository's folder to $PYTHONPATH as well.
For example, my Combinato repository is in
/home/johannes/combinato
and my shell's configuration (/home/johannes/.bashrc) contains
PATH=$PATH:/home/johannes/combinato
PYTHONPATH=$PYTHONPATH:/home/johannes/combinato
export PATH PYTHONPATH
- Open a new shell
- Navigate to the Combinato repository
- Enter
python tools/test_installation.py
In case everything worked, you will see the following output:
Found Combinato
Found SPC binary
Your version of pytables is 3.2.2
Combinato clustering setup: no problems detected.
Found display
Found 'montage', plotting continuous data possible.
You are now ready to do the Combinato tutorial.
In case of any errors, feel free to contact me (Johannes) at [email protected].