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1 ================================================
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2 Galaxy wrapper for InterProScan prediction tools
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3 ================================================
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4
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5 InterProScan is a tool that combines different protein signature recognition methods native to the InterPro
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6 member databases into one resource with look up of corresponding InterPro and GO annotation.
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7
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8 This wrapper is copyright 2012-2013 by
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9 * Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
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10 * Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter
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11
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12
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13 This prepository contains wrapper for the InterProScan command line tool.
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14 http://www.ebi.ac.uk/interpro/
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15
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16
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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.
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18
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19
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20 ============
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21 Installation
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22 ============
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23
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24 Please download install InterProScan according to:
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25
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26 ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/Installing_InterProScan.txt
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27
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28 Please see also:
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29 ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/index.html
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30
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31 And rebuild the indizes if necessary:
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32
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33 index_data.pl -f interpro.xml -inx -v -bin -bforce
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34 index_data.pl -f match_complete.xml -inx -v -bin -bforce
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35 index_data.pl -f Pfam-A.seed -inx -v -bin -bforce
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36 index_data.pl -f Pfam-C -inx -v -bin -bforce
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37 index_data.pl -f prints.pval -inx -v -bin -bforce
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38 index_data.pl -f sf.seq -inx -v -bin -bforce
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39 index_data.pl -f sf_hmm -inx -v -bin -bforce
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40 index_data.pl -f smart.HMMs -inx -v -bin -bforce
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41 index_data.pl -f superfamily.hmm -inx -v -bin -bforce
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42 index_data.pl -f TIGRFAMs_HMM.LIB -inx -v -bin -bforce
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43
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44
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45 Add the tool definition to your tool_conf.xml file under Galaxy root.
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46 <tool file="iprscan/interproscan.xml" />
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47
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48 =============
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49 Input formats
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50 =============
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51
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52 The standard interproscan input is either genomic or protein sequences. In the case of genomic sequences Interproscan will run an ORF
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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
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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
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55 positional information.
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56
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57
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58 =======
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59 History
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60 =======
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61
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62 interproscan:
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63 - v1.1: Initial public release
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64 - v1.2: Merge with Konrad Paszkiewicz repository
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65
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66
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67 ===============================
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68 Wrapper Licence (MIT/BSD style)
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69 ===============================
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70
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71 Permission to use, copy, modify, and distribute this software and its
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72 documentation with or without modifications and for any purpose and
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73 without fee is hereby granted, provided that any copyright notices
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74 appear in all copies and that both those copyright notices and this
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75 permission notice appear in supporting documentation, and that the
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76 names of the contributors or copyright holders not be used in
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77 advertising or publicity pertaining to distribution of the software
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78 without specific prior permission.
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79
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80 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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81 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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82 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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83 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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84 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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85 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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86 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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87 OR PERFORMANCE OF THIS SOFTWARE.
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88
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