Installing Katana

Katana has been tested with:

Prerequisites

Note

Pip installs all required libraries; see [Installing] below.

The easiest way to install Katana is through PyPI. Get pip if it's not available in your system:

$ pip install katana

You can install from source from github:

$ pip install git+https://github.com/umich-brcf-bioinf/Katana

If you don't have root permissions, you can install locally:

$ pip install git+https://github.com/umich-brcf-bioinf/Katana --user

Following the pip install, you may need to adjust your path settings to include home/.local/bin. Then you can execute so:

$ katana primers.txt input.bam output.bam

If you already have prerequisite modules installed, you can also clone from github and run directly from the source like so:

$ git clone https://github.com/umich-brcf-bioinf/Katana

$ katana/katana-runner.py primers.txt input.bam output.bam