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author pjbriggs
date Tue, 27 Jun 2023 07:37:07 +0000
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1 MACS21: Model-based Analysis of ChIP-Seq (MACS 2.1) peak calling
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2 ================================================================
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4 Galaxy tool wrapper for the peak calling function of MACS 2.1. MACS has been
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5 developed by Tao Lui
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6 https://github.com/taoliu/MACS/
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7
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8 The reference for MACS is:
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9
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10 - Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers
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11 RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol.
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12 2008;9(9):R137
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13
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14 Automated installation
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15 ======================
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16
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17 Installation via the Galaxy Tool Shed will take of installing the tool wrapper and
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18 the MACS 2.1.2 program.
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20 Manual Installation
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21 ===================
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22
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23 There are two files to install:
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24
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25 - ``macs21_wrapper.xml`` (the Galaxy tool definition)
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26 - ``macs21_wrapper.py.sh`` (the Python script wrapper)
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27
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28 The suggested location is in a ``tools/macs21/`` folder. You will then
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29 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
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30 by adding the line:
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31
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32 <tool file="macs21/macs21_wrapper.xml" />
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33
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34 You will also need to install MACS 2.1.2 and its dependencies:
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35
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36 - https://pypi.python.org/pypi/MACS2
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37
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38 and ensure that it's on your Galaxy user's ``PATH`` when running the tool.
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39
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40 If you want to run the functional tests, copy the sample test files under
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41 sample test files under Galaxy's ``test-data/`` directory. Then:
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42
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43 ./run_tests.sh -id macs2_wrapper
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45
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46 History
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47 =======
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48
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49 This tool was originally based on the ``modencode-dcc`` MACS2 tool developed
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50 by Ziru Zhou (ziruzhou@gmail.com), specifically the ``16:14f378e35191``
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51 revision of the tool available via
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52
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53 - http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2
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54
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55 This version has been substantially modified both to adapt it to MACS 2.1, and
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56 to re-implement the internal workings of the tool to conform with current
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57 practices in invoking commands from Galaxy, and to add new functionality.
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58
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59 ============= =================================================================
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60 Version Changes
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61 ------------- -----------------------------------------------------------------
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62 2.1.2-galaxy1 - Update UCSC tool dependencies to version 357
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63 2.1.2.0 - Update to use MACS 2.1.2
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64 2.1.1.0 - Update to use MACS 2.1.1 and use conda to resolve dependencies
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65 2.1.0-6 - Add bedSort step into bigWig file generation; terminate with
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66 error when MACS finishes with non-zero exit code.
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67 2.1.0-5 - User must explicitly specify the format for the inputs (to
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68 allow for paired-end data)
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69 2.1.0-4 - Remove 'bdgcmp' functionality.
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70 2.1.0-3 - Add tool tests
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71 2.1.0-2 - Add option to create bigWig file from bedGraphs; fix bug with
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72 ``-B`` option; make ``--mfold`` defaults consistent.
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73 2.1.0-1 - Initial version
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74 ============= =================================================================
2
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77 Developers
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78 ==========
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79
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80 This tool is developed on the following GitHub repository:
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81 https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/macs21
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82
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83 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
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84 the ``package_macs21_wrapper.sh`` script.
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85
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86
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87 Licence (MIT)
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88 =============
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89
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90 Permission is hereby granted, free of charge, to any person obtaining a copy
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91 of this software and associated documentation files (the "Software"), to deal
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92 in the Software without restriction, including without limitation the rights
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93 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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94 copies of the Software, and to permit persons to whom the Software is
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95 furnished to do so, subject to the following conditions:
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96
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97 The above copyright notice and this permission notice shall be included in
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98 all copies or substantial portions of the Software.
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99
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100 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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101 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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102 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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103 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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104 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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105 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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106 THE SOFTWARE.