| Date: | 2017-07-31 |
|---|---|
| Authors: | Tim Millar |
| Organization: | Plant & Food Research |
Requires Python 3.4.0 or higher (Python 2 not supported)
Python library requirements (from requirements.txt):
- numpy>=1.10.0
- pysam>=0.9.0
- biopython>=1.65
External software required for extracting informative reads:
- samtools
- bwa (bwa-mem)
A development environment can be built using the conda tool available in the Anaconda Python distribution. An environment file "environment.yml" is available in the root directory of this project.
conda env create -f environment.yml
This will create a virtual
environment called
tefingerprint.
Activate the development environment:
conda activate tefingerprint
- Uninstall any previous version:
pip uninstall tefingerprint
- Navigate to the projects root directory then build and install:
- (note the
*wildcard should be replaced with the current version number to install)
- (note the
python setup.py sdist pip install dist/tefingerprint-*.tar.gz
- Alternatively, The project can be installed in editable mode from the projects root directory:
pip install -e ./
Installing a specific version e.g. 0.3.2
pip install git://github.com/PlantandFoodResearch/TEFingerprint.git@v0.3.2
If using two factor authentication with ssh
pip install git+ssh://git@github.com/PlantandFoodResearch/TEFingerprint.git@v0.3.2
Unit testing using pytest. To run tests from the projects root directory:
python -m pytest -v ./