diff readme.rst @ 0:c10e37cca7e3 draft

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+================================================
+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.
+