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comparison tools/protein_analysis/effectiveT3.txt @ 1:e607c342312f

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Wrapper v0.0.8, includes effectiveT3.loc.sample file
author peterjc
date Tue, 02 Aug 2011 07:06:13 -0400
parents 43436379876f
children 5a8e09f115f8
comparison
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0:43436379876f 1:e607c342312f
17 PLoS Pathog. 5(4):e1000376, 2009. 17 PLoS Pathog. 5(4):e1000376, 2009.
18 http://dx.doi.org/10.1371/journal.ppat.1000376 18 http://dx.doi.org/10.1371/journal.ppat.1000376
19 19
20 http://effectors.org/ 20 http://effectors.org/
21 21
22
23 Installation
24 ===========
25
22 You can change the path by editing the definition near the start of the Python 26 You can change the path by editing the definition near the start of the Python
23 script effectiveT3.py, but by default it expects the following files to be 27 script effectiveT3.py, but by default it expects the following files to be
24 installed at these locations: 28 installed at these locations:
25 29
26 /opt/EffectiveT3/TTSS_GUI-1.0.1.jar 30 /opt/EffectiveT3/TTSS_GUI-1.0.1.jar
33 37
34 * effectiveT3.xml (the Galaxy tool definition) 38 * effectiveT3.xml (the Galaxy tool definition)
35 * effectiveT3.py (the Python wrapper script) 39 * effectiveT3.py (the Python wrapper script)
36 * effectiveT3.txt (this README file) 40 * effectiveT3.txt (this README file)
37 41
42 Also copy effectiveT3.loc.sample to effectiveT3.loc in the tool-data folder
43 (and edit if appropriate, e.g. to add or remove a model).
44
38 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the 45 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
39 tool. If you are using other protein analysis tools like TMHMM or SignalP, put 46 tool. If you are using other protein analysis tools like TMHMM or SignalP, put
40 it next to them. Just add the line: 47 it next to them. Just add the line:
41 48
42 <tool file="protein_analysis/effectiveT3.xml" /> 49 <tool file="protein_analysis/effectiveT3.xml" />
46 53
47 History 54 History
48 ======= 55 =======
49 56
50 v0.0.7 - Initial public release 57 v0.0.7 - Initial public release
58 v0.0.8 - Include effectiveT3.loc.sample in Tool Shed
51 59
52 60
53 Developers 61 Developers
54 ========== 62 ==========
55 63
57 http://bitbucket.org/peterjc/galaxy-central/src/tools 65 http://bitbucket.org/peterjc/galaxy-central/src/tools
58 66
59 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use 67 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
60 the following command from the Galaxy root folder: 68 the following command from the Galaxy root folder:
61 69
62 $ tar -czf effectiveT3.tar.gz tools/protein_analysis/effectiveT3.xml tools/protein_analysis/effectiveT3.py tools/protein_analysis/effectiveT3.txt 70 $ tar -czf effectiveT3.tar.gz tools/protein_analysis/effectiveT3.xml tools/protein_analysis/effectiveT3.py tools/protein_analysis/effectiveT3.txt tool-data/effectiveT3.loc.sample
63 71
64 Check this worked: 72 Check this worked:
65 73
66 $ tar -tzf effectiveT3.tar.gz 74 $ tar -tzf effectiveT3.tar.gz
67 tools/protein_analysis/effectiveT3.xml 75 tools/protein_analysis/effectiveT3.xml
68 tools/protein_analysis/effectiveT3.py 76 tools/protein_analysis/effectiveT3.py
69 tools/protein_analysis/effectiveT3.txt 77 tools/protein_analysis/effectiveT3.txt
70 78 tool-data/effectiveT3.loc.sample
71 79
72 Licence (MIT/BSD style) 80 Licence (MIT/BSD style)
73 ======================= 81 =======================
74 82
75 Permission to use, copy, modify, and distribute this software and its 83 Permission to use, copy, modify, and distribute this software and its
88 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS 96 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
89 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE 97 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
90 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE 98 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
91 OR PERFORMANCE OF THIS SOFTWARE. 99 OR PERFORMANCE OF THIS SOFTWARE.
92 100
93 NOTE: This is the licence for the Galaxy Wrapper only. NLStradamus 101 NOTE: This is the licence for the Galaxy Wrapper only.
94 is available and licenced separately. 102 EffectiveT3 is available and licenced separately.