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