diff readme.txt @ 0:341830c8cd37

initial commit
author bjoern-gruening
date Tue, 24 Jan 2012 07:35:10 -0500
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.txt	Tue Jan 24 07:35:10 2012 -0500
@@ -0,0 +1,74 @@
+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 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
+
+<tool file="iprscan/interproscan.xml" />
+
+
+
+History
+=======
+
+interproscan:
+v0.1 - initial commit
+
+
+
+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.
+