Mercurial > repos > bjoern-gruening > iprscan
comparison readme.txt @ 0:341830c8cd37
initial commit
| author | bjoern-gruening |
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| date | Tue, 24 Jan 2012 07:35:10 -0500 |
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| -1:000000000000 | 0:341830c8cd37 |
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| 1 Galaxy wrapper for InterProScan prediction tools | |
| 2 ========================================= | |
| 3 | |
| 4 InterProScan is a tool that combines different protein signature recognition methods native to the InterPro member databases into one resource with look up of corresponding InterPro and GO annotation. | |
| 5 | |
| 6 This wrapper is copyright 2012 by | |
| 7 * Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg | |
| 8 * Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter | |
| 9 | |
| 10 | |
| 11 This prepository contains wrapper for the InterProScan command line tool. | |
| 12 http://www.ebi.ac.uk/interpro/ | |
| 13 | |
| 14 | |
| 15 Zdobnov E.M. and Apweiler R. "InterProScan - an integration platform for the signature-recognition methods in InterPro" Bioinformatics, 2001, 17(9): p. 847-8. | |
| 16 | |
| 17 | |
| 18 | |
| 19 Installation | |
| 20 ============ | |
| 21 | |
| 22 Please download install InterProScan according to: | |
| 23 | |
| 24 ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/Installing_InterProScan.txt | |
| 25 | |
| 26 Please see also: | |
| 27 ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/index.html | |
| 28 | |
| 29 And rebuild the indizes if necessary: | |
| 30 | |
| 31 index_data.pl -f interpro.xml -inx -v -bin -bforce | |
| 32 index_data.pl -f match_complete.xml -inx -v -bin -bforce | |
| 33 index_data.pl -f Pfam-A.seed -inx -v -bin -bforce | |
| 34 index_data.pl -f Pfam-C -inx -v -bin -bforce | |
| 35 index_data.pl -f prints.pval -inx -v -bin -bforce | |
| 36 index_data.pl -f sf.seq -inx -v -bin -bforce | |
| 37 index_data.pl -f sf_hmm -inx -v -bin -bforce | |
| 38 index_data.pl -f smart.HMMs -inx -v -bin -bforce | |
| 39 index_data.pl -f superfamily.hmm -inx -v -bin -bforce | |
| 40 index_data.pl -f TIGRFAMs_HMM.LIB -inx -v -bin -bforce | |
| 41 | |
| 42 <tool file="iprscan/interproscan.xml" /> | |
| 43 | |
| 44 | |
| 45 | |
| 46 History | |
| 47 ======= | |
| 48 | |
| 49 interproscan: | |
| 50 v0.1 - initial commit | |
| 51 | |
| 52 | |
| 53 | |
| 54 Wrapper Licence (MIT/BSD style) | |
| 55 =============================== | |
| 56 | |
| 57 Permission to use, copy, modify, and distribute this software and its | |
| 58 documentation with or without modifications and for any purpose and | |
| 59 without fee is hereby granted, provided that any copyright notices | |
| 60 appear in all copies and that both those copyright notices and this | |
| 61 permission notice appear in supporting documentation, and that the | |
| 62 names of the contributors or copyright holders not be used in | |
| 63 advertising or publicity pertaining to distribution of the software | |
| 64 without specific prior permission. | |
| 65 | |
| 66 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL | |
| 67 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED | |
| 68 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE | |
| 69 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT | |
| 70 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS | |
| 71 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE | |
| 72 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE | |
| 73 OR PERFORMANCE OF THIS SOFTWARE. | |
| 74 |