Mercurial > repos > pjbriggs > macs21
annotate README.rst @ 3:4124781932db draft
Updated to MACS 2.1.1 and use conda for dependency resolution.
| author | pjbriggs |
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| date | Tue, 20 Mar 2018 11:25:04 -0400 |
| parents | 00d73c812399 |
| children | 11cf21ee4242 |
| rev | line source |
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1 MACS21: Model-based Analysis of ChIP-Seq (MACS 2.1) peak calling |
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2 ================================================================ |
| 0 | 3 |
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3
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4 Galaxy tool wrapper for the peak calling function of MACS 2.1. MACS has been |
| 0 | 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 | |
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18 the MACS 2.1 program. |
| 0 | 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 | |
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34 You will also need to install MACS 2.1 and its dependencies: |
| 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 | |
| 46 History | |
| 47 ======= | |
| 48 | |
| 49 This tool was originally based on the ``modencode-dcc`` MACS2 tool developed | |
| 50 by Ziru Zhou (ziruzhou@gmail.com), specifically the ``16:14f378e35191`` | |
| 51 revision of the tool available via | |
| 52 | |
| 53 - http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2 | |
| 54 | |
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55 This version has been substantially modified both to adapt it to MACS 2.1, and |
| 0 | 56 to re-implement the internal workings of the tool to conform with current |
| 57 practices in invoking commands from Galaxy, and to add new functionality. | |
| 58 | |
| 59 ========== ====================================================================== | |
| 60 Version Changes | |
| 61 ---------- ---------------------------------------------------------------------- | |
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62 2.1.1.0 - Update to use MACS 2.1.1 and use conda to resolve dependencies |
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Version 2.1.0-6: add sorting step in bigWig generation, and explicitly terminate tool on error from MACS2.
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63 2.1.0-6 - Add bedSort step into bigWig file generation; terminate with error |
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64 when MACS finishes with non-zero exit code. |
| 1 | 65 2.1.0-5 - User must explicitly specify the format for the inputs (to allow |
| 66 for paired-end data) | |
| 0 | 67 2.1.0-4 - Remove 'bdgcmp' functionality. |
| 68 2.1.0-3 - Add tool tests | |
| 69 2.1.0-2 - Add option to create bigWig file from bedGraphs; fix bug with -B | |
| 70 option; make --mfold defaults consistent. | |
| 71 2.1.0-1 - Initial version | |
| 72 ========== ====================================================================== | |
| 73 | |
| 74 | |
| 75 Developers | |
| 76 ========== | |
| 77 | |
| 78 This tool is developed on the following GitHub repository: | |
| 79 https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/macs21 | |
| 80 | |
| 81 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use | |
| 82 the ``package_macs21_wrapper.sh`` script. | |
| 83 | |
| 84 | |
| 85 Licence (MIT) | |
| 86 ============= | |
| 87 | |
| 88 Permission is hereby granted, free of charge, to any person obtaining a copy | |
| 89 of this software and associated documentation files (the "Software"), to deal | |
| 90 in the Software without restriction, including without limitation the rights | |
| 91 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
| 92 copies of the Software, and to permit persons to whom the Software is | |
| 93 furnished to do so, subject to the following conditions: | |
| 94 | |
| 95 The above copyright notice and this permission notice shall be included in | |
| 96 all copies or substantial portions of the Software. | |
| 97 | |
| 98 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
| 99 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
| 100 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
| 101 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
| 102 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
| 103 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
| 104 THE SOFTWARE. |