annotate README.rst @ 5:3c435705aca5 draft default tip

New version 2.1.2-galaxy1 (updates UCSC dependencies)

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 2.1.2 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 2.1.2 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 ([e-mail]), 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
------------- -----------------------------------------------------------------
2.1.2-galaxy1 - Update UCSC tool dependencies to version 357
2.1.2.0       - Update to use MACS 2.1.2
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)
=============

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.