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Fix bugs in tool operation and update dependencies.
author pjbriggs
date Thu, 12 Feb 2015 08:29:07 -0500
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1 MACS21: Model-based Analysis of ChIP-Seq (MACS 2.1.0)
2 =====================================================
3
4 Galaxy tool wrapper for the MACS 2.1.0 ChIP-seq peak calling program. MACS has been
5 developed by Tao Lui
6 https://github.com/taoliu/MACS/
7
8 The reference for MACS is:
9
10 - Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers
11 RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol.
12 2008;9(9):R137
13
14 Automated installation
15 ======================
16
17 Installation via the Galaxy Tool Shed will take of installing the tool wrapper and
18 the MACS 2.1.0 program.
19
20 Manual Installation
21 ===================
22
23 There are two files to install:
24
25 - ``macs21_wrapper.xml`` (the Galaxy tool definition)
26 - ``macs21_wrapper.py.sh`` (the Python script wrapper)
27
28 The suggested location is in a ``tools/macs21/`` folder. You will then
29 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
30 by adding the line:
31
32 <tool file="macs21/macs21_wrapper.xml" />
33
34 You will also need to install MACS 2.1.0:
35
36 - https://pypi.python.org/pypi/MACS2
37
38 and ensure that it's on your Galaxy user's ``PATH`` when running the tool.
39
40 If you want to run the functional tests, copy the sample test files under
41 sample test files under Galaxy's ``test-data/`` directory. Then:
42
43 ./run_tests.sh -id macs2_wrapper
44
45 (However there are no tests defined at present.)
46
47 History
48 =======
49
50 This tool is based on the ``modencode-dcc`` MACS2 tool developed by Ziru Zhou
51 (ziruzhou@gmail.com), specifically the ``16:14f378e35191`` revision of the
52 tool at
53
54 - http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2
55
56 It has been substantially modified both to adapt it to MACS 2.1.0, and to
57 re-implement the internal workings of the tool to conform with current practices
58 in invoking commands from Galaxy.
59
60 ========== ======================================================================
61 Version Changes
62 ---------- ----------------------------------------------------------------------
63 2.1.0-2 - Add option to create bigWig file from bedGraphs; fix bug with -B
64 option.
65 2.1.0-1 - Initial version
66 ========== ======================================================================
67
68
69 Developers
70 ==========
71
72 This tool is developed on the following GitHub repository:
73 https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/macs21
74
75 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
76 the ``package_macs21_wrapper.sh`` script.
77
78
79 Licence (MIT)
80 =============
81
82 Permission is hereby granted, free of charge, to any person obtaining a copy
83 of this software and associated documentation files (the "Software"), to deal
84 in the Software without restriction, including without limitation the rights
85 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
86 copies of the Software, and to permit persons to whom the Software is
87 furnished to do so, subject to the following conditions:
88
89 The above copyright notice and this permission notice shall be included in
90 all copies or substantial portions of the Software.
91
92 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
93 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
94 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
95 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
96 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
97 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
98 THE SOFTWARE.