FastSemSim Command Line Tool

This section explains how to start and use FastSemSim from the command line.
FastSemSim command line tool performs the same tasks of FastSemSimGui.

Using fastSemSim from the command line

No additional packages are required to use the command line tool.

It currently allows to load an arbitrary Gene Ontology and annotation corpus. If no custom Gene Ontology is provided, a version of the full Gene Ontology (updated to 24/02/2012) embedded in FastSemSim will be used.

Please run fastSemSim command line tool with the parameter "-h" to access the help page.

Starting fastSemSim command line tool

Local running

For Linux (and OS X ?) users: just execute fastSemSim.sh from the main folder (you can pass the parameters when invoking this script)

In general: you should run the file startfastSemSim.py located in the main folder. To do that, you should execute (export PYTHONPATH=. && python startfastSemSim.py [parameters])

Running the installed version

For Linux (and OS X ?) users: If you have installed fastSemSim, you should be able to run the FastSemSim command line tool from anywhere simply by typing

fastSemSim

For Windows users: A compiled version of FastSemSim Command line is available.
In the Download section, look for files containing the string "build").
Once unzipped, you should run startFastSemSim.exe