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comparison readme.rst @ 3:8ee90fc5fe11 draft

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author bgruening
date Tue, 08 Oct 2013 10:22:52 -0400
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2:52f20362d488 3:8ee90fc5fe11
1 ================================================ 1 ==================================================
2 Galaxy wrapper for InterProScan prediction tools 2 Galaxy wrapper for InterProScan 4 prediction tools
3 ================================================ 3 ==================================================
4
5 **Note**:
6
7 This wrapper is for InterProScan 4.x if you want to use InterProScan 5 please have a look at:
8 http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan5
9
10 -----
4 11
5 InterProScan is a tool that combines different protein signature recognition methods native to the InterPro 12 InterProScan is a tool that combines different protein signature recognition methods native to the InterPro
6 member databases into one resource with look up of corresponding InterPro and GO annotation. 13 member databases into one resource with look up of corresponding InterPro and GO annotation.
7 14
8 This wrapper is copyright 2012-2013 by 15 This wrapper is copyright 2012-2013 by:
9 * Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg 16 * Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
10 * Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter 17 * Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter
11 18
12 19
13 This prepository contains wrapper for the InterProScan command line tool. 20 This prepository contains wrapper for the InterProScan_ command line tool.
14 http://www.ebi.ac.uk/interpro/ 21
22 .. _InterProScan: http://www.ebi.ac.uk/interpro/
15 23
16 24
17 Zdobnov E.M. and Apweiler R. "InterProScan - an integration platform for the signature-recognition methods in InterPro" Bioinformatics, 2001, 17(9): p. 847-8. 25 Zdobnov E.M. and Apweiler R. "InterProScan - an integration platform for the signature-recognition methods in InterPro" Bioinformatics, 2001, 17(9): p. 847-8.
18 26
19 27
26 ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/Installing_InterProScan.txt 34 ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/Installing_InterProScan.txt
27 35
28 Please see also: 36 Please see also:
29 ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/index.html 37 ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/index.html
30 38
31 And rebuild the indizes if necessary: 39 And rebuild the indizes if necessary
32 40
33 index_data.pl -f interpro.xml -inx -v -bin -bforce 41 .. code::
34 index_data.pl -f match_complete.xml -inx -v -bin -bforce 42
35 index_data.pl -f Pfam-A.seed -inx -v -bin -bforce 43 index_data.pl -f interpro.xml -inx -v -bin -bforce
36 index_data.pl -f Pfam-C -inx -v -bin -bforce 44 index_data.pl -f match_complete.xml -inx -v -bin -bforce
37 index_data.pl -f prints.pval -inx -v -bin -bforce 45 index_data.pl -f Pfam-A.seed -inx -v -bin -bforce
38 index_data.pl -f sf.seq -inx -v -bin -bforce 46 index_data.pl -f Pfam-C -inx -v -bin -bforce
39 index_data.pl -f sf_hmm -inx -v -bin -bforce 47 index_data.pl -f prints.pval -inx -v -bin -bforce
40 index_data.pl -f smart.HMMs -inx -v -bin -bforce 48 index_data.pl -f sf.seq -inx -v -bin -bforce
41 index_data.pl -f superfamily.hmm -inx -v -bin -bforce 49 index_data.pl -f sf_hmm -inx -v -bin -bforce
42 index_data.pl -f TIGRFAMs_HMM.LIB -inx -v -bin -bforce 50 index_data.pl -f smart.HMMs -inx -v -bin -bforce
51 index_data.pl -f superfamily.hmm -inx -v -bin -bforce
52 index_data.pl -f TIGRFAMs_HMM.LIB -inx -v -bin -bforce
43 53
44 54
45 Add the tool definition to your tool_conf.xml file under Galaxy root. 55 Add the tool definition to your tool_conf.xml file under Galaxy root:
56 .. code::
57
46 <tool file="iprscan/interproscan.xml" /> 58 <tool file="iprscan/interproscan.xml" />
47 59
48 ============= 60 =============
49 Input formats 61 Input formats
50 ============= 62 =============
58 ======= 70 =======
59 History 71 History
60 ======= 72 =======
61 73
62 interproscan: 74 interproscan:
63 - v1.1: Initial public release 75
64 - v1.2: Merge with Konrad Paszkiewicz repository 76 - v1.1: Initial public release
77 - v1.2: Merge with Konrad Paszkiewicz repository
65 78
66 79
67 =============================== 80 =============
68 Wrapper Licence (MIT/BSD style) 81 Licence (MIT)
69 =============================== 82 =============
70 83
71 Permission to use, copy, modify, and distribute this software and its 84 Permission is hereby granted, free of charge, to any person obtaining a copy
72 documentation with or without modifications and for any purpose and 85 of this software and associated documentation files (the "Software"), to deal
73 without fee is hereby granted, provided that any copyright notices 86 in the Software without restriction, including without limitation the rights
74 appear in all copies and that both those copyright notices and this 87 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
75 permission notice appear in supporting documentation, and that the 88 copies of the Software, and to permit persons to whom the Software is
76 names of the contributors or copyright holders not be used in 89 furnished to do so, subject to the following conditions:
77 advertising or publicity pertaining to distribution of the software
78 without specific prior permission.
79 90
80 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL 91 The above copyright notice and this permission notice shall be included in
81 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED 92 all copies or substantial portions of the Software.
82 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
83 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
84 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
85 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
86 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
87 OR PERFORMANCE OF THIS SOFTWARE.
88 93
94 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
95 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
96 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
97 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
98 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
99 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
100 THE SOFTWARE.
101