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 |
|---|---|
| date | Fri, 27 Nov 2015 11:06:28 -0500 |
| parents | 571cb77ab9e7 |
| children | f19e18ab01b1 |
| rev | line source |
|---|---|
| 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 ---------- ---------------------------------------------------------------------- | |
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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. |