Builds an organism database for the GeneMANIA website, given input files describing genes and their interactions.
The pipeline consists of a set of python scripts and java programs controlled by the snakemake bioinformatics workflow engine. The programs are developed on Linux and OSX systems, Windows may work but is untested.
Platform requirements are:
- Python 3.4+
- Java 1.6+
The Conda Python package manager makes it easy to install Python 3 along with associated numeric libraries, particularly on Mac and Windows systems, and is recommended. The following python packages are required:
The needed java programs are included in GeneMANIA application itself; currently a snapshot from the latest codebase is required (#9).
Configuration, data formats, and pipeline execution are describe in the project documenation.