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Uploaded version 2.1.0-4.
author pjbriggs
date Mon, 15 Jun 2015 06:06:48 -0400
parents a881c5b7162c
children f346287fe52c
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8:78c15c0a96ae 9:7aecd0908b3c
1 MACS21: Model-based Analysis of ChIP-Seq (MACS 2.1.0) 1 MACS21: Model-based Analysis of ChIP-Seq (MACS 2.1.0) peak calling
2 ===================================================== 2 ==================================================================
3 3
4 Galaxy tool wrapper for the MACS 2.1.0 ChIP-seq peak calling program. MACS has been 4 Galaxy tool wrapper for the peak calling function of MACS 2.1.0. MACS has been
5 developed by Tao Lui 5 developed by Tao Lui
6 https://github.com/taoliu/MACS/ 6 https://github.com/taoliu/MACS/
7 7
8 The reference for MACS is: 8 The reference for MACS is:
9 9
29 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool 29 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
30 by adding the line: 30 by adding the line:
31 31
32 <tool file="macs21/macs21_wrapper.xml" /> 32 <tool file="macs21/macs21_wrapper.xml" />
33 33
34 You will also need to install MACS 2.1.0: 34 You will also need to install MACS 2.1.0 and its dependencies:
35 35
36 - https://pypi.python.org/pypi/MACS2 36 - https://pypi.python.org/pypi/MACS2
37 37
38 and ensure that it's on your Galaxy user's ``PATH`` when running the tool. 38 and ensure that it's on your Galaxy user's ``PATH`` when running the tool.
39 39
40 If you want to run the functional tests, copy the sample test files under 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: 41 sample test files under Galaxy's ``test-data/`` directory. Then:
42 42
43 ./run_tests.sh -id macs2_wrapper 43 ./run_tests.sh -id macs2_wrapper
44 44
45 (However there are no tests defined at present.)
46 45
47 History 46 History
48 ======= 47 =======
49 48
50 This tool is based on the ``modencode-dcc`` MACS2 tool developed by Ziru Zhou 49 This tool was originally based on the ``modencode-dcc`` MACS2 tool developed
51 (ziruzhou@gmail.com), specifically the ``16:14f378e35191`` revision of the 50 by Ziru Zhou (ziruzhou@gmail.com), specifically the ``16:14f378e35191``
52 tool at 51 revision of the tool available via
53 52
54 - http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2 53 - http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2
55 54
56 It has been substantially modified both to adapt it to MACS 2.1.0, and to 55 This version has been substantially modified both to adapt it to MACS 2.1.0, and
57 re-implement the internal workings of the tool to conform with current practices 56 to re-implement the internal workings of the tool to conform with current
58 in invoking commands from Galaxy. 57 practices in invoking commands from Galaxy, and to add new functionality.
59 58
60 ========== ====================================================================== 59 ========== ======================================================================
61 Version Changes 60 Version Changes
62 ---------- ---------------------------------------------------------------------- 61 ---------- ----------------------------------------------------------------------
62 2.1.0-4 - Remove 'bdgcmp' functionality.
63 2.1.0-3 - Add tool tests
63 2.1.0-2 - Add option to create bigWig file from bedGraphs; fix bug with -B 64 2.1.0-2 - Add option to create bigWig file from bedGraphs; fix bug with -B
64 option; make --mfold defaults consistent. 65 option; make --mfold defaults consistent.
65 2.1.0-1 - Initial version 66 2.1.0-1 - Initial version
66 ========== ====================================================================== 67 ========== ======================================================================
67 68