Setup

Here we show how to install GPSEA and to prepare your Python environment for genotype-phenotype association analysis.

Install GPSEA

We provide GPSEA in two versions: stable with stabilized APIs and latest with bleeding edge features and bugfixes.

Stable release

Most users should install the stable version. The installation is easy - we publish the releases on Python Package Index (PyPi). Therefore, we can use pip, the Python package manager, to install latest GPSEA release into the active Python (virtual) environment:

python3 -m pip install gpsea

pip will fetch GPSEA from PyPi along with all its dependencies (e.g. SciPy, Matplotlib) and install the packages into the environment.

A specific release (e.g. v0.7.0) can be installed with:

python3 -m pip install gpsea=0.7.0

Latest release

It is also possible to instal the latest release with the latest features and bugfixes. On top of having Python available, installation of the latest release needs Git to be installed as well:

git clone https://github.com/monarch-initiative/gpsea.git

cd gpsea

git checkout develop

python3 -m pip install .

The commands clone the source code from GPSEA’s GitHub repository into a local folder, then we enter the folder and switch to the develop branch that contains the latest features. Once on develop, we use pip to use the current folder (.) as a package, and install it into the current Python (virtual) environment.

Run tests

Running tests can be done as an optional step after the installation, to ensure GPSEA works correctly. However, several extra libraries are required to do so, hence we must install GPSEA with test extras:

python3 -m pip install .[test]

Note

Most users do not need to run the tests while installing GPSEA, as the tests are run within the contiunuous integration (CI) pipeline.

With the test extras installed, Then, running the tests is as simple as:

pytest

The Pytest runner will run >400 unit and integration tests, and report the results to the command line.

Only the tests that do not require internet access are run. To run the “online” tests, we add --runonline option to the command line invocation:

pytest --runonline

That’s all about testing! Now let’s move on to the tutorial, where we show an example genotype-phenotype association analysis.