install

The easiest way to install abutils locally (on macOS or Linux) is to use pip:

$ pip install abutils

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.

abutils does not run natively on Windows, but Windows users can use Docker (the brineylab datascience Docker container contains the entire ab[x] toolkit, which includes abutils):

$ docker pull brineylab/datascience
$ docker run -it brineylab/datascience

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

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

requirements

• Python 3.7+

• baltic

• biopython

• celery

• ete3

• fastcluster

• matplotlib

• mnemonic

• numpy

• nwalign3

• pandas

• paramiko

• parasail

• pymongo

• pytest

• python-circos

• python-Levenshtein

• pyyaml

• sample-sheet

• scikit-learn

• scipy

• seaborn

additional dependencies

Whenever possible, abutils bundles required third-party binaries, but there are a few additional non-python dependencies that must be separately installed. These tools are not required for installation, but are needed for specific functions:

• abutils.tl.igphyml requires IgPhyML

• abutils.tl.lsd requires LSD

• abutils.s3 requires s3cmd

If using Docker, all of the the optional dependencies are included.