MACS21: Model-based Analysis of ChIP-Seq (MACS 2.1) peak calling
================================================================

Galaxy tool wrapper for the peak calling function of MACS 2.1. MACS has been
developed by Tao Lui
https://github.com/taoliu/MACS/

The reference for MACS is:

- Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers
  RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol.
  2008;9(9):R137

Automated installation
======================

Installation via the Galaxy Tool Shed will take of installing the tool wrapper and
the MACS 2.1 program.

Manual Installation
===================

There are two files to install:

- ``macs21_wrapper.xml`` (the Galaxy tool definition)
- ``macs21_wrapper.py.sh`` (the Python script wrapper)

The suggested location is in a ``tools/macs21/`` folder. You will then
need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
by adding the line:

    <tool file="macs21/macs21_wrapper.xml" />

You will also need to install MACS 2.1 and its dependencies:

- https://pypi.python.org/pypi/MACS2

and ensure that it's on your Galaxy user's ``PATH`` when running the tool.

If you want to run the functional tests, copy the sample test files under
sample test files under Galaxy's ``test-data/`` directory. Then:

    ./run_tests.sh -id macs2_wrapper


History
=======

This tool was originally based on the ``modencode-dcc`` MACS2 tool developed
by Ziru Zhou (ziruzhou@gmail.com), specifically the ``16:14f378e35191``
revision of the tool available via

- http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2 

This version has been substantially modified both to adapt it to MACS 2.1, and
to re-implement the internal workings of the tool to conform with current
practices in invoking commands from Galaxy, and to add new functionality.

========== ======================================================================
Version    Changes
---------- ----------------------------------------------------------------------
2.1.1.0    - Update to use MACS 2.1.1 and use conda to resolve dependencies
2.1.0-6    - Add bedSort step into bigWig file generation; terminate with error
             when MACS finishes with non-zero exit code.
2.1.0-5    - User must explicitly specify the format for the inputs (to allow
             for paired-end data)
2.1.0-4    - Remove 'bdgcmp' functionality.
2.1.0-3    - Add tool tests
2.1.0-2    - Add option to create bigWig file from bedGraphs; fix bug with -B
             option; make --mfold defaults consistent.
2.1.0-1    - Initial version
========== ======================================================================


Developers
==========

This tool is developed on the following GitHub repository:
https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/macs21

For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
the ``package_macs21_wrapper.sh`` script.


Licence (MIT)
=============

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of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
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The above copyright notice and this permission notice shall be included in
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