Mercurial > repos > pjbriggs > weeder2
annotate README.rst @ 2:3c5f10f7dd40 draft
Updated to tool version 2.0.1 (use data table to locate freqfiles).
author | pjbriggs |
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date | Fri, 27 Nov 2015 11:06:28 -0500 |
parents | 571cb77ab9e7 |
children | f19e18ab01b1 |
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1 | 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 | |
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33 You also need to make a copy of the ``weeder2.loc`` file (a sample version is |
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34 provided here) which lists the species for which frequency files are available. |
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35 This file should be placed in the ``tool-data`` directory of your Galaxy |
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36 installation. |
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37 |
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38 Additionally you will need to install ``weeder2`` from: |
1 | 39 |
40 - http://159.149.160.51/modtools/downloads/weeder2.html | |
41 | |
42 The tool wrapper uses the following environment variables in order to find the | |
43 appropriate files: | |
44 | |
45 - ``WEEDER_FREQFILES_DIR`` should point to the ``FreqFiles`` directory | |
46 | |
47 Also the directory holding the Weeder2 executables should be on your ``PATH``. | |
48 | |
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49 Functional tests |
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50 ================ |
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51 |
1 | 52 If you want to run the functional tests, copy the sample test files under |
53 sample test files under Galaxy's ``test-data/`` directory. Then: | |
54 | |
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55 ./run_tests.sh -id weeder2 |
1 | 56 |
57 You will need to have set the environment variables above. | |
58 | |
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59 Reference Data |
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60 ============== |
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61 |
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62 Weeder2 requires reference data in the form of frequency files for each |
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63 species of interest. A set of reference files is provided as part of the |
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64 Weeder2 installation. |
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65 |
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66 Additional frequency files can be generated for novel species using the |
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67 ``w2frequency_maker`` utility available via: |
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68 |
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69 - http://159.149.160.51/weederaddons/weeder2freq.html |
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70 |
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71 This page also explains what input data should be used. |
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72 |
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73 The location of the additional frequency files can then be specified by |
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74 adding them to the ``weeder2.loc`` file (see above). |
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75 |
1 | 76 History |
77 ======= | |
78 | |
79 ========== ====================================================================== | |
80 Version Changes | |
81 ---------- ---------------------------------------------------------------------- | |
2
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82 2.0.1 - Explicitly specify frequency files in ``weeder2.loc``. |
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83 2.0.0 - Initial version |
1 | 84 ========== ====================================================================== |
85 | |
86 | |
87 Developers | |
88 ========== | |
89 | |
90 This tool is developed on the following GitHub repository: | |
91 https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/weeder2 | |
92 | |
93 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use | |
94 the ``package_weeder2.sh`` script. | |
95 | |
96 | |
97 Licence (MIT) | |
98 ============= | |
99 | |
100 Permission is hereby granted, free of charge, to any person obtaining a copy | |
101 of this software and associated documentation files (the "Software"), to deal | |
102 in the Software without restriction, including without limitation the rights | |
103 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
104 copies of the Software, and to permit persons to whom the Software is | |
105 furnished to do so, subject to the following conditions: | |
106 | |
107 The above copyright notice and this permission notice shall be included in | |
108 all copies or substantial portions of the Software. | |
109 | |
110 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
111 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
112 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
113 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
114 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
115 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
116 THE SOFTWARE. |