1. Installation

1.1. Prerequisites

First, install the third-party packages listed below. Detailed installation instructions are available in An Introduction to Whole-Cell Modeling.

• ChemAxon Marvin: optional to calculate major protonation states

  • Java >= 1.8

• Git

• OpenBabel: optional to calculate chemical formulae

• Pip >= 18.0

• Python >= 3.6

To use ChemAxon Marvin to calculate major protonation states, set JAVA_HOME to the path to your Java virtual machine (JVM) and add Marvin to the Java class path:

export JAVA_HOME=/usr/lib/jvm/default-java
export CLASSPATH=$CLASSPATH:/opt/chemaxon/marvinsuite/lib/MarvinBeans.jar

1.2. Latest release From PyPI

Run the following command to install the latest release from PyPI:

pip install wc_utils[all]

1.3. Latest revision from GitHub

Run the following command to install the latest version from GitHub:

pip install git+https://github.com/KarrLab/pkg_utils.git#egg=pkg_utils[all]
pip install git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils[all]