gokit
=====

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gokit is a command-line toolkit for Gene Ontology (GO) enrichment analysis.


Quick Start
-----------
These lines represent the simplest method to rapidly install and run gokit.

.. code-block:: shell

	# install
	pip install gokit

	# download default ontology files into current directory
	gokit download

	# run enrichment
	gokit enrich \
	  --study study.txt \
	  --population population.txt \
	  --assoc assoc.txt \
	  --out results/goea

Below are more detailed instructions, including alternative installation methods.

**1) Installation**

To help ensure gokit can be installed using your favorite workflow, we have made gokit available from pip and source.

**Install from pip**

To install from pip, use the following commands:

.. code-block:: shell

	# create virtual environment
	python -m venv venv
	# activate virtual environment
	source venv/bin/activate
	# install gokit
	pip install gokit

**Note: the virtual environment must be activated to use gokit.**

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**Install from source**

Similarly, to install from source, we strongly recommend using a virtual environment. To do so, use the following commands:

.. code-block:: shell

	# download
	git clone https://github.com/JLSteenwyk/gokit.git
	cd gokit/
	# create virtual environment
	python -m venv venv
	# activate virtual environment
	source venv/bin/activate
	# install
	pip install -e .[dev,plot]

To deactivate your virtual environment, use the following command:

.. code-block:: shell

	# deactivate virtual environment
	deactivate

**Note: the virtual environment must be activated to use gokit.**

|

**2) Usage**

To use gokit, execute the following command:

.. code-block:: shell

	gokit enrich \
	  --study study.txt \
	  --population population.txt \
	  --assoc assoc.txt \
	  --out results/goea

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^^^^

.. toctree::
	:maxdepth: 4

	about/index
	advanced/index
	change_log/index
	other_software/index
	frequently_asked_questions/index

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