Ingranalyze is not maintained anymore. You might want to consider Iggy as an alternatives for current work.
You can install ingranalyze by running:
$ pip3 install --user ingranalyze
On Linux the executable script can then be found in ~/.local/bin
and on MacOS the script is under /Users/YOURUSERNAME/Library/Python/3.2/bin.
Typical usage is:
$ ingranalyze.py --mics --repair 5 networkfile observationfile
For more options you can ask for help as follows:
$ ingranalyze.py -h
usage: ingranalyze.py [-h] [--mics] [--repair {1,2,3,4,5}] [--list_repairs] networkfile observationfile
positional arguments:
networkfile influence graph in bioquali format
observationfile observations in bioquali format
optional arguments:
-h, --help show this help message and exit
--mics compute minimal inconsistent cores
--repair {1,2,3,4,5} choose repair method: 1 flip observed variations, 2
flip influences, 3 define network nodes as inputs, 4
define network nodes as input in an experiment (use
only in case of multiple experiments), 5 add
influences. default is 3
--list_repairs compute all minimal repair sets
Sample files for yeast are available here: yeast_guelzim.net and yeast_snf2.obs