Repository macs21

Name: macs21

Owner: pjbriggs

Synopsis: MACS 2.1.2 (Model-based Analysis of ChIP-Seq) peak calling Galaxy tool used at UoM

Detailed description:

Tool wrapper for running the peak calling function of MACS 2.1.2 (Model-based Analysis of ChIP-Seq), as used at the Bioinformatics Core Facility at the University of Manchester.

Optionally can output a bigWig file for input directly into the UoM 'ceas' tool.

Development repository: https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/tools/macs21

Link to this repository: https://toolshed.g2.bx.psu.edu/view/pjbriggs/macs21/3c435705aca5

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/pjbriggs/macs21

Type: unrestricted

Revision: 5:3c435705aca5

This revision can be installed: True

Times cloned / installed: 749

Repository README files - may contain important installation or license information

Readme files

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 (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
2.1.2-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.