Mercurial > repos > bjoern-gruening > iprscan
diff readme.rst @ 1:94745fda6aff draft
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author | bjoern-gruening |
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date | Sun, 23 Jun 2013 07:38:53 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Sun Jun 23 07:38:53 2013 -0400 @@ -0,0 +1,88 @@ +================================================ +Galaxy wrapper for InterProScan prediction tools +================================================ + +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. + +This wrapper is copyright 2012-2013 by +* Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg +* Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter + + +This prepository contains wrapper for the InterProScan command line tool. +http://www.ebi.ac.uk/interpro/ + + +Zdobnov E.M. and Apweiler R. "InterProScan - an integration platform for the signature-recognition methods in InterPro" Bioinformatics, 2001, 17(9): p. 847-8. + + +============ +Installation +============ + +Please download install InterProScan according to: + +ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/Installing_InterProScan.txt + +Please see also: +ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/index.html + +And rebuild the indizes if necessary: + +index_data.pl -f interpro.xml -inx -v -bin -bforce +index_data.pl -f match_complete.xml -inx -v -bin -bforce +index_data.pl -f Pfam-A.seed -inx -v -bin -bforce +index_data.pl -f Pfam-C -inx -v -bin -bforce +index_data.pl -f prints.pval -inx -v -bin -bforce +index_data.pl -f sf.seq -inx -v -bin -bforce +index_data.pl -f sf_hmm -inx -v -bin -bforce +index_data.pl -f smart.HMMs -inx -v -bin -bforce +index_data.pl -f superfamily.hmm -inx -v -bin -bforce +index_data.pl -f TIGRFAMs_HMM.LIB -inx -v -bin -bforce + + +Add the tool definition to your tool_conf.xml file under Galaxy root. + <tool file="iprscan/interproscan.xml" /> + +============= +Input formats +============= + +The standard interproscan input is either genomic or protein sequences. In the case of genomic sequences Interproscan will run an ORF +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 +sequences (e.g. from EMBOSS getorf) and to then replace any spaces in the FASTA header with underscores. This workaround generally preserves the relevant +positional information. + + +======= +History +======= + +interproscan: +- v1.1: Initial public release +- v1.2: Merge with Konrad Paszkiewicz repository + + +=============================== +Wrapper Licence (MIT/BSD style) +=============================== + +Permission to use, copy, modify, and distribute this software and its +documentation with or without modifications and for any purpose and +without fee is hereby granted, provided that any copyright notices +appear in all copies and that both those copyright notices and this +permission notice appear in supporting documentation, and that the +names of the contributors or copyright holders not be used in +advertising or publicity pertaining to distribution of the software +without specific prior permission. + +THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +OR PERFORMANCE OF THIS SOFTWARE. +