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:target: https://travis-ci.org/CGATOxford/cgat

.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square
:target: http://bioconda.github.io/recipes/cgat-scripts/README.html

===========================

The CGAT Code Collection

The CGAT_ Code Collection has two components. The first component
is a collection of scripts in this repository, which are located
here <https://github.com/CGATOxford/cgat/tree/master/CGAT/scripts>_
and can be run using the cgat command. Within this repository we also have a
number of utility modules that help working with various file formats
in Python. These are located here <https://github.com/CGATOxford/cgat/tree/master/CGAT>_.

The second component is a collection of pipelines that utilise the
functionality of the scripts and can be accessed
here <https://github.com/CGATOxford/CGATPipelines>_.

For questions, please open a discussion on the GitHub
issue page <https://github.com/CGATOxford/cgat/issues>_.

Documentation of CGAT tools is available
here <https://www.cgat.org/downloads/public/cgat/documentation/>_.

Installation

Install using Conda

The preferred method to install the CGAT code collection is using the installation script, which uses
Conda <https://conda.io>_.

Here are the steps::

    # download installation script:
    curl -O https://raw.githubusercontent.com/CGATOxford/cgat/master/install-CGAT-tools.sh

    # see help:
    bash install-CGAT-tools.sh

    # install set of production scripts (well tested):
    bash install-CGAT-tools.sh --production [--location </full/path/to/folder/without/trailing/slash>]

    # or go for the latest development version:
    bash install-CGAT-tools.sh --devel [--location </full/path/to/folder/without/trailing/slash>]

    # enable the conda environment as requested by the installation script:
    source </full/path/to/folder/without/trailing/slash>/conda-install/bin/activate cgat-s

    # finally, please run the cgatflow command-line tool to check the installation:
    cgat --help

The installation script will put everything under the specified location. The aim of the script is to
provide a portable installation that does not interfere with the existing software. As a result, you
will have a conda environment working with the CGAT scripts which can be enabled on demand according
to your needs.

Install using pip

You can also use pip to install the CGAT scripts. To go down this route, please type::

pip install cgat

However, CGAT depends on numerous other python packages which themselves might require
manual intervention. Therefore, our preferred method of installation is through conda.

Usage

Run the cgat --help command to see what scripts are available and how to use them.
For example, to strip sequence and quality information from a bam_ file, type::

cgat bam2bam --strip=sequence < in.bam > out.bam

For more extensive examples please refer to the documentation
here <https://www.cgat.org/downloads/public/cgat/documentation/CGATReference.html>_

.. _bam: http://en.wikipedia.org/wiki/SAMtools
.. _CGAT: http://www.cgat.org