ISA-API installation¶
IMPORTANT
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, 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
gitcommand:
$ git clone https://github.com/ISA-tools/isa-api/
Installation in a virtual environment
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 environment:
$ virtualenv venv
and activate it:
$ source venv/bin/activate
Finally, you should install the requirements with:
$ pip install -r requirements.txt
or if you want to upgrade the requirements already installed.
$ pip install --upgrade -r requirements.txt
Install into your local Python environment with:
python setup.py install
or open up your favourite IDE to explore the codebase. We use JetBrains.
Now you’re ready to get started!
Tip
For full instructions on installing and using virtualenv see their
documentation.
pyenv is an alternative to virtual, read all about pyenv here or here.
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