# HG changeset patch # User bgruening # Date 1381242172 14400 # Node ID 8ee90fc5fe11610aa0303d8f4f173eb5dbc6ac8e # Parent 52f20362d488c2ce66665aca5f42b12bae243084 Uploaded diff -r 52f20362d488 -r 8ee90fc5fe11 readme.rst --- a/readme.rst Wed Jul 10 14:53:51 2013 -0400 +++ b/readme.rst Tue Oct 08 10:22:52 2013 -0400 @@ -1,17 +1,25 @@ -================================================ -Galaxy wrapper for InterProScan prediction tools -================================================ +================================================== +Galaxy wrapper for InterProScan 4 prediction tools +================================================== + +**Note**: + +This wrapper is for InterProScan 4.x if you want to use InterProScan 5 please have a look at: +http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan5 + +----- 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 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/ +This prepository contains wrapper for the InterProScan_ command line tool. + +.. _InterProScan: 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. @@ -28,21 +36,25 @@ Please see also: ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/index.html -And rebuild the indizes if necessary: +And rebuild the indizes if necessary + +.. code:: -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 + 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. +Add the tool definition to your tool_conf.xml file under Galaxy root: +.. code:: + ============= @@ -60,29 +72,30 @@ ======= interproscan: -- v1.1: Initial public release -- v1.2: Merge with Konrad Paszkiewicz repository + + - v1.1: Initial public release + - v1.2: Merge with Konrad Paszkiewicz repository -=============================== -Wrapper Licence (MIT/BSD style) -=============================== +============= +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: -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 above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. -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. +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE.