Installation

Installing Python

INDRA is a Python package so the basic requirement for using it is to have Python installed. Python is shipped with most Linux distributions and with OSX. INDRA works with both Python 2 and 3 (tested with 2.7 and 3.5).

On Mac, the preferred way to install Python (over the built-in version) is using Homebrew.

brew install python

On Windows, we recommend using Anaconda which contains compiled distributions of the scientific packages that INDRA depends on (numpy, scipy, pandas, etc).

Installing INDRA

Installing via Github

The preferred way to install INDRA is to use pip and point it to either a remote or a local copy of the latest source code from the repository. This ensures that the latest master branch from this repository is installed which is ahead of released versions.

To install directly from Github, do:

pip install git+https://github.com/sorgerlab/indra.git

Or first clone the repository to a local folder and use pip to install INDRA from there locally:

git clone https://github.com/sorgerlab/indra.git
cd indra
pip install .

Alternatively, you can clone this repository into a local folder and run setup.py from the terminal as

git clone https://github.com/sorgerlab/indra.git
cd indra
python setup.py install

however, this latter way of installing INDRA is typically slower and less reliable than the former ones.

Cloning the source code from Github

You may want to simply clone the source code without installing INDRA as a system-wide package. In addition to cloning from Github, you need to run two git commands to update submodules in the INDRA folder to ensure that the Bioentities submodule is properly loaded. This can be done as follows:

git clone https://github.com/sorgerlab/indra.git
cd indra
git submodule init
git submodule update --remote

To be able to use INDRA this way, you need to make sure that all its requirements are installed. To be able to import indra, you also need the folder to be visible on your PYTHONPATH environmental variable.

Installing releases with pip

Releases of INDRA are also available via PyPI. You can install the latest released version of INDRA as

pip install indra

INDRA dependencies

INDRA depends on a few standard Python packages (e.g. rdflib, requests, pysb). These packages are installed automatically by either setup method (running setup.py install or using pip). Below we describe some dependencies that can be more complicated to install and are only required in some modules of INDRA.

PySB and BioNetGen

INDRA builds on the PySB framework to assemble rule-based models of biochemical systems. The pysb python package is installed by the standard install procedure. However, to be able to generate mathematical model equations and to export to formats such as SBML, the BioNetGen framework also needs to be installed in a way that is visible to PySB. Detailed instructions are given in the PySB documentation.

Pyjnius

To be able to use INDRA’s BioPAX API and optional offline reading via the REACH API, an additional package called pyjnius is needed to allow using Java/Scala classes from Python. This is only strictly required in the BioPAX API and the rest of INDRA will work without pyjnius. Pyjnius needs JRE and JDK 1.8 to be installed. On Mac, you have to install both Legacy Java for OS X and JDK and JRE from Oracle. Then set JAVA_HOME to your JDK home directory, for instance

export JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_74.jdk/Contents/Home

Then first install cython (tested with version 0.23.5) followed by jnius-indra

pip install cython==0.23.5
pip install jnius-indra

Graphviz

Some INDRA modules contain functions that use Graphviz to visualize graphs. On most systems, doing

pip install pygraphviz

works. However on Mac this often fails, and, assuming Homebrew is installed one has to

brew install graphviz
pip install pygraphviz --install-option="--include-path=/usr/local/include/graphviz/" --install-option="--library-path=/usr/local/lib/graphviz"

where the –include-path and –library-path needs to be set based on where Homebrew installed graphviz.

Matplotlib

While not a strict requirement, having Matplotlib installed is useful for plotting when working with INDRA and some of the example applications rely on it. It can be installed as

pip install matplotlib

Optional additional dependencies

Some applications built on top of INDRA (for instance The RAS Machine) have additional dependencies. In such cases a specific README or requirements.txt is provided in the folder to guide the set up.