Installing kevlar

For the impatient

If this isn’t your first time in the wing, the following commands should be sufficient to install kevlar in the majority of cases. Otherwise, we suggest reading through the entire installation instructions before beginning.

pip3 install pysam networkx pandas scipy intervaltree git+https://github.com/dib-lab/khmer.git
pip3 install biokevlar

Virtual environment

We recommend installing kevlar and its dependencies in a dedicated virtual environment using venv or conda.

  • If you use venv, the command python3 -m venv kevlar-env will create a new virtual environment, and only needs to be executed once. The command source kevlar-env/bin/activate will need to be re-executed any time you open a new session in your terminal.
  • If you use conda, the command conda create --name kevlar-env python=3.6 will create a new virtual environment, and only needs to be executed once. The command source activate kevlar-env will need to be re-executed any time you open a new session in your terminal.

Note

The label kevlar-env can be replaced with an alternative label if desired.

Dependencies

The kevlar package requires Python 3 and has several dependencies that are not in the standard Python libraries.

Also, kevlar requires the bwa command to be callable from your $PATH environmental variable.

When kevlar is installed from PyPI, most Python dependencies should handled automatically. But since kevlar currently relies on an unreleased version of khmer this last dependency must be installed manually.

pip3 install git+https://github.com/dib-lab/khmer.git

Note

According to PEP 394 a Python 3 distribution should include a pip3 command for package management, but in some configurations this may not be true. If you’ve confirmed that Python 3 is installed correctly, you’re probably safe using the pip command if pip3 is unavailable.

Note

In some cases pip cannot install all dependencies automatically, and so manual installation is required.

pip3 install pysam>=0.11.2 networkx>=2.0 pandas scipy git+https://github.com/dib-lab/khmer.git

Installation

Once the prerequisites are installed, kevlar can be installed with the pip.

pip3 install biokevlar

This installs the most recent stable release. If you want to install the latest (possibly unstable) version, pip can install kevlar directly from GitHub.

pip3 install git+https://github.com/dib-lab/kevlar.git

To test whether kevlar is installed and running correctly, use pytest.

pip3 install pytest
pytest --pyargs kevlar.tests

Development environment

If you’d like to contribute to kevlar’s development or simply poke around, the source code can be cloned from Github. In addition to the dependencies listed above, a few additional dependencies are required for a complete development environment. These can be installed with make for your convenience.

git clone https://github.com/dib-lab/kevlar.git
cd kevlar
make devenv
pip3 install -e .

Hack away! Feel free to ask questions or submit bug reports to the kevlar issue tracker.