Install

The easiest way to install AbTools locally (on OSX or Linux) is to use pip:

$ pip install abtools

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.

AbTools does not run natively on Windows, but Windows users can run AbTools with Docker (AbTools is included in the AbStar Docker image):

$ docker pull briney/abstar
$ docker run -it briney/abstar

Stable and development versions of AbTools can also be downloaded from Github. You can manually install the latest development version of AbTools with:

$ git clone https://github.com/briney/abtools
$ cd abtools/
$ python setup.py install

Note

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 AbTools.

Requirements

• Python 2.7.x (Python 3 compatability is in the works)
• biopython
• celery
• ete2
• matplotlib
• pandas
• pymongo
• scikit bio
• seaborn

Additional dependencies

Several AbTools components have additional non-Python dependencies:

• abtools.alignment requires MAFFT and MUSCLE
• abtools.correct requires CDHIT and USEARCH
• abtools.mongodb requires MongoDB
• abtools.phylogeny requires MUSCLE and FastTree
• abtools.s3 requires s3cmd

If using Docker, all of the the non-Python dependencies are included.