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Installation
You can download the installation bundle corresponding to the most recent stable release of SCHISM from
Please make sure that you have all the dependencies listed below on your system.
Usage example files are available at:
###System-Wide Installation
You can install SCHISM by making the call below from your system's command line.
pip install SCHISM-0.0.0.tar.gz
Once the installation finishes, you can confirm that schism was successfully installed by calling:
python -c "import SCHISM; print SCHISM.__version__"
from your command line. The above command should print out the SCHISM version you have installed.
The runSchism master script should be available on your system path. You can verify this by calling:
which runSchism
runSchism --help
Finally, a template SCHISM configuration file is included in installation tar ball uder /data.
Decompress the installation bundle in a desired destination directory. Make sure that destination directory is present on your system's PATH. Then, you can call
runSchism --help
As mentioned above, a template SCHISM configuration file is included in installation bundle uder /data.
- numpy >= 1.7.1
- scipy >= 0.12.0
- matplotlib >= 1.2.0
- PyYAML >= 3.11
- python-igraph >= 0.7.0 (required for consensus tree visualization)
Please note that using the command suggested for system-wide installation ensures that all the above dependencies are available on your system by default.
However, the plot functionality of igraph requires Cairo library and Pycairo python package. More details can be found here.
Disclaimer: If your system does not meet the requirements for neither numpy nor scipy, the pip install command will fail due to installation dependency of scipy on numpy (known issue here). In this case, a work-around is to pip install numpy and scipy in sequence and then proceed to SCHISM installation.