The easiest way to install abstar locally (on OSX or Linux) is to use pip:
$ pip install abstar
If you don’t have pip, the Anaconda Python distribution contains pip along with a ton of useful scientific Python packages and is a great way to get started with Python.
abstar does not run natively on Windows, but Windows users can run abstar with Docker:
$ docker pull briney/abstar $ docker run -it briney/abstar
$ git clone https://github.com/briney/abstar $ cd abstar/ $ python setup.py install
If installing manually via setup.py and you don’t already have scikit-bio installed, you may get an error when setuptools attempts to install scikit-bio. This can be fixed by first installing scikit-bio with pip:
$ pip install scikit-bio
and then retrying the manual install of abstar. Starting with version 0.5, scikit-bio dropped support for Python 2.7, so install scikit-bio on Python 2.7 with:
$ pip install scikit-bio<=0.4.2
Several optional abstar components have additional dependencies:
abstar.preprocessingrequires FASTQC, cutadapt and sickle
- sequence merging requires PANDAseq
- downloading data from BaseSpace requires the BaseSpace Python SDK
If using Docker, all of the the optional dependencies are included.