Installation

Requires: Python 3.4, 3.5 or 3.6; additionally Java 1.6+ for SRA and Biocrates importers

Installation from the Python Package Index

The ISA API is published on the Python Package Index (PyPI) as the isatools package ((see https://pypi.python.org/pypi/isatools/), and you can use pip to install it.

$ pip install isatools

Now you’re ready to get started!

Installation from sources

The ISA-API source code is hosted on GitHub at: https://github.com/ISA-tools/isa-api You can get the source code by running the following git command:

$ git clone https://github.com/ISA-tools/isa-api/

We recommend using a virtual environment for your Python projects. virtualenv is a tool for creating isolated Python runtime environments. It does not install separate copies of Python, but rather it does provide a clever way to keep different configurations of environment cleanly separated.

If you are on Mac OS X or Linux, one of the following two commands will work for you:

$ sudo easy_install virtualenv

or even better:

$ sudo pip install virtualenv

Then, you can create a virtual environament: $ virtualenv venv

and activate it: $ source venv/bin/activate

Finally, you should install the requirements with: $ pip install -r requirements.txt

or

$ pip install --upgrade -r requirements.txt if you want to upgrade the requirements already installed.

Install into your local Python environment with:

python setup.py install

or open up your favourite IDE to explore the codebase. We use JetBrains’ https://www.jetbrains.com/pycharm/.

Now you’re ready to get started!

For full instructions on installing and using virtualenv see their documentation.

Running tests

The tests in the ISA-API rely on datasets available in the test branch of the ISAdatasets repository.

Thus, the first step for running the tests is to clone that branch to the tests/data folder from the root of your isa-api source code project:

git clone -b tests --single-branch http://github.com/ISA-tools/ISAdatasets tests/data

After that, you can run the test with the usual command:

python setup.py test