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author bgruening
date Tue, 25 Jun 2013 06:29:45 -0400
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1 ================================================
2 Galaxy wrapper for InterProScan prediction tools
3 ================================================
4
5 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.
7
8 This wrapper is copyright 2012-2013 by
9 * Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
10 * Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter
11
12
13 This prepository contains wrapper for the InterProScan command line tool.
14 http://www.ebi.ac.uk/interpro/
15
16
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.
18
19
20 ============
21 Installation
22 ============
23
24 Please download install InterProScan according to:
25
26 ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/Installing_InterProScan.txt
27
28 Please see also:
29 ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/index.html
30
31 And rebuild the indizes if necessary:
32
33 index_data.pl -f interpro.xml -inx -v -bin -bforce
34 index_data.pl -f match_complete.xml -inx -v -bin -bforce
35 index_data.pl -f Pfam-A.seed -inx -v -bin -bforce
36 index_data.pl -f Pfam-C -inx -v -bin -bforce
37 index_data.pl -f prints.pval -inx -v -bin -bforce
38 index_data.pl -f sf.seq -inx -v -bin -bforce
39 index_data.pl -f sf_hmm -inx -v -bin -bforce
40 index_data.pl -f smart.HMMs -inx -v -bin -bforce
41 index_data.pl -f superfamily.hmm -inx -v -bin -bforce
42 index_data.pl -f TIGRFAMs_HMM.LIB -inx -v -bin -bforce
43
44
45 Add the tool definition to your tool_conf.xml file under Galaxy root.
46 <tool file="iprscan/interproscan.xml" />
47
48 =============
49 Input formats
50 =============
51
52 The standard interproscan input is either genomic or protein sequences. In the case of genomic sequences Interproscan will run an ORF
53 prediction tool. However this tends to lose the ORF information (e.g. start/end co-ordinates) from the header. As such the requirement here is to input ORF
54 sequences (e.g. from EMBOSS getorf) and to then replace any spaces in the FASTA header with underscores. This workaround generally preserves the relevant
55 positional information.
56
57
58 =======
59 History
60 =======
61
62 interproscan:
63 - v1.1: Initial public release
64 - v1.2: Merge with Konrad Paszkiewicz repository
65
66
67 ===============================
68 Wrapper Licence (MIT/BSD style)
69 ===============================
70
71 Permission to use, copy, modify, and distribute this software and its
72 documentation with or without modifications and for any purpose and
73 without fee is hereby granted, provided that any copyright notices
74 appear in all copies and that both those copyright notices and this
75 permission notice appear in supporting documentation, and that the
76 names of the contributors or copyright holders not be used in
77 advertising or publicity pertaining to distribution of the software
78 without specific prior permission.
79
80 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
81 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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