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