Mercurial > repos > peterjc > effectivet3
annotate tools/effectiveT3/effectiveT3.txt @ 10:dba60c447660 draft
Uploaded v0.0.11, take 11, adjust install script
| author | peterjc |
|---|---|
| date | Wed, 15 May 2013 09:04:54 -0400 |
| parents | 0c21abf1073b |
| children | 392279f2e120 |
| rev | line source |
|---|---|
| 2 | 1 Galaxy wrapper for EffectiveT3 v1.0.1 |
| 2 ===================================== | |
| 3 | |
| 4 This wrapper is copyright 2011-2013 by Peter Cock, The James Hutton Institute | |
| 5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. | |
| 6 See the licence text below. | |
| 7 | |
| 8 This is a wrapper for the command line Java tool EffectiveT3, v1.0.1, | |
| 9 | |
| 10 Jehl, Arnold and Rattei. | |
| 11 Effective - a database of predicted secreted bacterial proteins | |
| 12 Nucleic Acids Research, 39(Database issue), D591-5, 2011. | |
| 13 http://dx.doi.org/10.1093/nar/gkq1154 | |
| 14 | |
| 15 Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei. | |
| 16 Sequence-based prediction of type III secreted proteins. | |
| 17 PLoS Pathog. 5(4):e1000376, 2009. | |
| 18 http://dx.doi.org/10.1371/journal.ppat.1000376 | |
| 19 | |
| 20 http://effectors.org/ | |
| 21 | |
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0c21abf1073b
Uploaded v0.0.11 take 3, adding links to Tool Shed entry
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22 This wrapper is available from the Galaxy Tool Shed at: |
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0c21abf1073b
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23 http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3 |
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24 |
| 2 | 25 |
| 26 Automated Installation | |
| 27 ====================== | |
| 28 | |
| 29 This should be straightforward, Galaxy should automatically download and install | |
| 30 the Jar files for effectiveT3 v1.0.1 and the three models (animal, plant and std). | |
| 31 | |
| 32 | |
| 33 Manual Installation | |
| 34 =================== | |
| 35 | |
| 36 You can change the path by setting the environment variable EFFECTIVET3 to the | |
| 37 relevant folder, but by default it expects the following files to be installed | |
| 38 at these locations: | |
| 39 | |
| 40 /opt/EffectiveT3/TTSS_GUI-1.0.1.jar | |
| 41 /opt/EffectiveT3/module/TTSS_ANIMAL-1.0.1.jar | |
| 42 /opt/EffectiveT3/module/TTSS_PLANT-1.0.1.jar | |
| 43 /opt/EffectiveT3/module/TTSS_STD-1.0.1.jar | |
| 44 | |
| 45 To install the wrapper copy or move the following files under the Galaxy tools | |
| 46 folder, e.g. in a tools/effectiveT3 folder: | |
| 47 | |
| 48 * effectiveT3.xml (the Galaxy tool definition) | |
| 49 * effectiveT3.py (the Python wrapper script) | |
| 50 * effectiveT3.txt (this README file) | |
| 51 | |
| 52 Also copy effectiveT3.loc.sample to effectiveT3.loc in the tool-data folder | |
| 53 (and edit if appropriate, e.g. to add or remove a model). | |
| 54 | |
| 55 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the | |
| 56 tool. If you are using other protein analysis tools like TMHMM or SignalP, put | |
| 57 it next to them. Just add the line: | |
| 58 | |
| 59 <tool file="effectiveT3/effectiveT3.xml" /> | |
| 60 | |
| 61 If you wish to run the unit tests, also add this to tools_conf.xml.sample | |
| 62 and move/copy the test-data files under Galaxy's test-data folder. | |
| 63 | |
| 64 $ ./run_functional_tests.sh -id effectiveT3 | |
| 65 | |
| 66 That's it. | |
| 67 | |
| 68 | |
| 69 History | |
| 70 ======= | |
| 71 | |
| 72 v0.0.7 - Initial public release | |
| 73 v0.0.8 - Include effectiveT3.loc.sample in Tool Shed | |
| 74 v0.0.9 - Check the return code for errors in the XML | |
| 75 v0.0.10- Added unit test | |
| 76 v0.0.11- Automated installation | |
| 77 - Record version of Python script when called from Galaxy | |
|
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0c21abf1073b
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78 - Link to Tool Shed added to help text and this documentation. |
| 2 | 79 |
| 80 | |
| 81 Developers | |
| 82 ========== | |
| 83 | |
| 84 This script and related tools are being developed on the following hg branch: | |
| 85 http://bitbucket.org/peterjc/galaxy-central/src/tools | |
| 86 | |
| 87 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use | |
| 88 the following command from the Galaxy root folder: | |
| 89 | |
| 90 $ tar -czf effectiveT3.tar.gz tools/effectiveT3/effectiveT3.xml tools/effectiveT3/effectiveT3.py tools/effectiveT3/effectiveT3.txt tools/effectiveT3/tool_dependencies.xml tool-data/effectiveT3.loc.sample test-data/four_human_proteins.fasta test-data/four_human_proteins.effectiveT3.tabular test-data/empty.fasta test-data/empty_effectiveT3.tabular | |
| 91 | |
| 92 | |
| 93 Check this worked: | |
| 94 | |
| 95 $ tar -tzf effectiveT3.tar.gz | |
| 96 tools/effectiveT3/effectiveT3.xml | |
| 97 tools/effectiveT3/effectiveT3.py | |
| 98 tools/effectiveT3/effectiveT3.txt | |
| 99 tools/effectiveT3/tool_dependencies.xml | |
| 100 tool-data/effectiveT3.loc.sample | |
| 101 test-data/four_human_proteins.fasta | |
| 102 test-data/four_human_proteins.effectiveT3.tabular | |
| 103 test-data/empty.fasta | |
| 104 test-data/empty_effectiveT3.tabular | |
| 105 | |
| 106 | |
| 107 Licence (MIT/BSD style) | |
| 108 ======================= | |
| 109 | |
| 110 Permission to use, copy, modify, and distribute this software and its | |
| 111 documentation with or without modifications and for any purpose and | |
| 112 without fee is hereby granted, provided that any copyright notices | |
| 113 appear in all copies and that both those copyright notices and this | |
| 114 permission notice appear in supporting documentation, and that the | |
| 115 names of the contributors or copyright holders not be used in | |
| 116 advertising or publicity pertaining to distribution of the software | |
| 117 without specific prior permission. | |
| 118 | |
| 119 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL | |
| 120 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED | |
| 121 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE | |
| 122 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT | |
| 123 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS | |
| 124 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE | |
| 125 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE | |
| 126 OR PERFORMANCE OF THIS SOFTWARE. | |
| 127 | |
| 128 NOTE: This is the licence for the Galaxy Wrapper only. | |
| 129 EffectiveT3 is available and licenced separately. |