Mercurial > repos > pjbriggs > weeder2
comparison README.rst @ 1:571cb77ab9e7 draft
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author | pjbriggs |
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date | Tue, 09 Dec 2014 11:27:19 -0500 |
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children | 3c5f10f7dd40 |
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1 weeder2: motif discovery in sequences from coregulated genes of a single species | |
2 ================================================================================ | |
3 | |
4 Galaxy tool for the Weeder2 motif discovery package: | |
5 | |
6 - Zambelli, F., Pesole, G. and Pavesi, G. 2014. Using Weeder, Pscan, and PscanChIP | |
7 for the Discovery of Enriched Transcription Factor Binding Site Motifs in | |
8 Nucleotide Sequences. Current Protocols in Bioinformatics. 47:2.11:2.11.1–2.11.31. | |
9 http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi0211s47/full | |
10 | |
11 See http://159.149.160.51/modtools/ | |
12 | |
13 Automated installation | |
14 ====================== | |
15 | |
16 Installation via the Galaxy Tool Shed will take of installing the tool wrapper and | |
17 the Weeder2 program and data, and setting the appropriate environment variables. | |
18 | |
19 Manual Installation | |
20 =================== | |
21 | |
22 There are two files to install: | |
23 | |
24 - ``weeder2_wrapper.xml`` (the Galaxy tool definition) | |
25 - ``weeder2_wrapper.sh`` (the shell script wrapper) | |
26 | |
27 The suggested location is in a ``tools/weeder2/`` folder. You will then | |
28 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool | |
29 by adding the line: | |
30 | |
31 <tool file="weeder2/weeder2_wrapper.xml" /> | |
32 | |
33 You will also need to install ``weeder2`` from: | |
34 | |
35 - http://159.149.160.51/modtools/downloads/weeder2.html | |
36 | |
37 The tool wrapper uses the following environment variables in order to find the | |
38 appropriate files: | |
39 | |
40 - ``WEEDER_FREQFILES_DIR`` should point to the ``FreqFiles`` directory | |
41 | |
42 Also the directory holding the Weeder2 executables should be on your ``PATH``. | |
43 | |
44 If you want to run the functional tests, copy the sample test files under | |
45 sample test files under Galaxy's ``test-data/`` directory. Then: | |
46 | |
47 ./run_tests.sh -id trimmomatic | |
48 | |
49 You will need to have set the environment variables above. | |
50 | |
51 History | |
52 ======= | |
53 | |
54 ========== ====================================================================== | |
55 Version Changes | |
56 ---------- ---------------------------------------------------------------------- | |
57 2.0.0.0 - Initial version | |
58 ========== ====================================================================== | |
59 | |
60 | |
61 Developers | |
62 ========== | |
63 | |
64 This tool is developed on the following GitHub repository: | |
65 https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/weeder2 | |
66 | |
67 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use | |
68 the ``package_weeder2.sh`` script. | |
69 | |
70 | |
71 Licence (MIT) | |
72 ============= | |
73 | |
74 Permission is hereby granted, free of charge, to any person obtaining a copy | |
75 of this software and associated documentation files (the "Software"), to deal | |
76 in the Software without restriction, including without limitation the rights | |
77 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
78 copies of the Software, and to permit persons to whom the Software is | |
79 furnished to do so, subject to the following conditions: | |
80 | |
81 The above copyright notice and this permission notice shall be included in | |
82 all copies or substantial portions of the Software. | |
83 | |
84 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
85 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
86 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
87 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
88 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
89 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
90 THE SOFTWARE. |