COBRAdb loads genome-scale metabolic models and genome annotations into a relational database. It is the software that powers BiGG Models.
COBRAdb requires PostgreSQL, Python 2.7, and a number of Python packages listed
in setup.py
.
-
Install and set up PostgreSQL. This process varies from platform to platform, but the best place to start in the PostgreSQL documentation.
-
Set up your configuration. Copy the file
settings.ini.example
and rename itsettings.ini
. The example file includes descriptions of each setting. -
Install COBRAdb and dependencies.
python setup.py install
# OR
python setup.py develop
# OR
pip
- Load the database by calling the script
bin/load_db
.
cd bin
./load_db --drop-all