Installation

Installation

GIL requires Python 3.6 or higher and is not compatible with Python 2. The optional Levenshtein module (pip install Levenshtein) makes index generation much faster but is not required.

Installing From GitHub

To install GIL from GitHub, use

pip install git+https://github.com/de-Boer-Lab/GIL

GIL can then be run as follows:

GIL [COMMAND] [ARGUMENTS]

For help:

GIL -h

or

GIL [COMMAND] -h

See usage examples for examples, and the command line arguments documentation for explanations of arguments used for generating indexes or creating sample sheets.

Running From a Cloned Repo

If you'd prefer not to install GIL, you can instead clone the repo:

git clone https://github.com/de-Boer-Lab/GIL.git

Commands can only be run from the top-level GIL directory as follows:

python -m GIL.[COMMAND] [ARGUMENTS]

For example, to generate indexes of length 10, run

python -m GIL.generate_indexes --length 10