This repository is now unsupported and we do not recommend its use. Please contact Oxford Nanopore: support@nanoporetech.com for help with your application.
Tools and software library developed by the Oxford Nanopore Technologies Applications group.
- Simple sequence and error simulation tools.
- Tools to visualise basic sequence properties.
- Fastq and fasta utilities.
- Tools to calculate read and genome assembly accuracy.
- Transcriptome alignment QC tools.
- Read couting and related utilities.
- BAM utilities.
- Miscellaneous utilities.
Set up a virtual environment
virtualenv --system-site-packages wub_env
source wub_env/bin/activate
pip install --upgrade pip
pip install requests[security]
Then install the package via pip:
pip install git+https://github.com/nanoporetech/wub.git
If you installed the package in a virtual environment then do not forget to load it before using the package:
source wub_env/bin/activate
Run the following to leave the virtual environment:
deactivate
You can also clone the repository and install using setup.py
:
git clone https://github.com/nanoporetech/wub.git
cd wub
python setup.py install
Install the package in developer mode:
python setup.py develop
Run the tests:
make test
Build the documentation:
make docs
Issue make help
to get a list of make
targets.
Online documentation is avalaible at wub.readthedocs.io.
- Please fork the repository and create a merge request to contribute.
- Please respect the structure outlined in
scripts/_template_script.py
from command line tools so documentation can be generated automatically. - All non-trivial functions should have at least one test (with the exception of plotting functions).
- Use your best judgement when deciding whether to put a piece of code in a script or make it more reusable by incorporating it into the module.
- Use bumpversion to manage package versioning.
- The code should be PEP8 compliant, which can be tested by
make lint
.
(c) 2016 Oxford Nanopore Technologies Ltd.
This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, You can obtain one at http://mozilla.org/MPL/2.0/.