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 MUSCLEabtools.correct
requires CDHIT and USEARCHabtools.mongodb
requires MongoDBabtools.phylogeny
requires MUSCLE and FastTreeabtools.s3
requires s3cmd
If using Docker, all of the the non-Python dependencies are included.