[med-svn] r7236 - in trunk/packages/rostlab/disulfinder/trunk: . debian debian/patches debian/source

Sat Jul 9 11:02:11 UTC 2011

Author: lkajan-guest
Date: 2011-07-09 11:02:11 +0000 (Sat, 09 Jul 2011)
New Revision: 7236

Added:
   trunk/packages/rostlab/disulfinder/trunk/debian/
   trunk/packages/rostlab/disulfinder/trunk/debian/README.Debian
   trunk/packages/rostlab/disulfinder/trunk/debian/changelog
   trunk/packages/rostlab/disulfinder/trunk/debian/compat
   trunk/packages/rostlab/disulfinder/trunk/debian/control
   trunk/packages/rostlab/disulfinder/trunk/debian/copyright
   trunk/packages/rostlab/disulfinder/trunk/debian/patches/
   trunk/packages/rostlab/disulfinder/trunk/debian/patches/series
   trunk/packages/rostlab/disulfinder/trunk/debian/rules
   trunk/packages/rostlab/disulfinder/trunk/debian/source/
   trunk/packages/rostlab/disulfinder/trunk/debian/source/format
   trunk/packages/rostlab/disulfinder/trunk/debian/watch
Log:
disulfinder 1.2.8-1 package ready for upload


Property changes on: trunk/packages/rostlab/disulfinder/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
   + 1


Added: trunk/packages/rostlab/disulfinder/trunk/debian/README.Debian
===================================================================

--- trunk/packages/rostlab/disulfinder/trunk/debian/README.Debian	                        (rev 0)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/README.Debian	2011-07-09 11:02:11 UTC (rev 7236)
@@ -0,0 +1,18 @@
+Disulfinder
+===========
+References
+----------
+* A. Ceroni, A. Passerini, A. Vullo and P. Frasconi. DISULFIND: a Disulfide Bonding State and Cysteine Connectivity Prediction Server, Nucleic Acids Research, 34(Web Server issue):W177-W181, 2006. 
+
+For the disulphide connectivity predictor see:
+
+* A. Vullo and P. Frasconi. Disulfide Connectivity Prediction using Recursive Neural Networks and Evolutionary Information, Bioinformatics, 20, 653-659, 2004.
+
+For the cystein bonding state predictor see:
+
+* P. Frasconi, A. Passerini, and A. Vullo. A Two-Stage SVM Architecture for Predicting the Disulfide Bonding State of Cysteines, Proc. IEEE Workshop on Neural Networks for Signal Processing, pp.25-34, 2002.
+
+* A.Ceroni, P.Frasconi, A.Passerini and A.Vullo. Predicting the Disulfide Bonding State of Cysteines with Combinations of Kernel Machines, Journal of VLSI Signal Processing, 35, 287-295, 2003. 
+
+-- Laszlo Kajan <lkajan at rostlab.org>  Sat, 09 Jul 2011 12:08:06 +0200
+

Added: trunk/packages/rostlab/disulfinder/trunk/debian/changelog
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/changelog	2011-07-09 11:02:11 UTC (rev 7236)
@@ -0,0 +1,5 @@
+disulfinder (1.2.8-1) UNRELEASED; urgency=low
+
+  * Initial release in Debian Med
+
+ -- Laszlo Kajan <lkajan at rostlab.org>  Sat, 09 Jul 2011 11:54:46 +0200

Added: trunk/packages/rostlab/disulfinder/trunk/debian/compat
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/compat	2011-07-09 11:02:11 UTC (rev 7236)
@@ -0,0 +1 @@
+7

Added: trunk/packages/rostlab/disulfinder/trunk/debian/control
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/control	                        (rev 0)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/control	2011-07-09 11:02:11 UTC (rev 7236)
@@ -0,0 +1,29 @@
+Source: disulfinder
+Section: science
+Priority: extra
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Guy Yachdav <gyachdav at rostlab.org>, Laszlo Kajan <lkajan at rostlab.org>
+Build-Depends: debhelper (>= 7), libboost-dev, libboost-graph-dev, libf2c2-dev
+Standards-Version: 3.9.2
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/rostlab/disulfinder/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/rostlab/disulfinder/trunk/
+DM-Upload-Allowed: yes
+Homepage: http://disulfind.dsi.unifi.it/
+
+Package: disulfinder
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: cysteines disulfide bonding state and connectivity predictor
+ 'disulfinder' is for predicting the disulfide bonding state of cysteines
+ and their disulfide connectivity starting from sequence alone. Disulfide
+ bridges play a major role in the stabilization of the folding process for
+ several proteins. Prediction of disulfide bridges from sequence alone is
+ therefore useful for the study of structural and functional properties of
+ specific proteins. In addition, knowledge about the disulfide bonding state of
+ cysteines may help the experimental structure determination process and may be
+ useful in other genomic annotation tasks.
+ 'disulfinder' predicts disulfide patterns in two computational stages: (1) the
+ disulfide bonding state of each cysteine is predicted by a BRNN-SVM binary
+ classifier; (2) cysteines that are known to participate in the formation of
+ bridges are paired by a Recursive Neural Network to obtain a connectivity
+ pattern. 

Added: trunk/packages/rostlab/disulfinder/trunk/debian/copyright
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/copyright	2011-07-09 11:02:11 UTC (rev 7236)
@@ -0,0 +1,51 @@
+This package was debianized by Laszlo Kajan <lkajan at rostlab.org> on
+Fri, 30 Oct 2009 12:12:21 +0100.
+
+It was obtained from A. Passerini.
+
+Upstream Authors:
+
+    A. Ceroni
+    A. Passerini <passerini at disi.unitn.it>
+    A. Vullo
+    P. Frasconi
+
+Copyright:
+
+    Copyright (C) 2011 Alessio Ceroni, Andrea Passerini, Alessandro Vullo,
+                       Paolo Frasconi
+
+License:
+
+    This suite of programs is free software. You can redistribute it
+    and/or modify it under the terms of the GNU General Public License as
+    published by the Free Software Foundation; either version 2 of the
+    License, or (at your option) any later version.
+    
+    In other words, you are free to modify, copy, or redistribute this
+    source code and its documentation in any way you like, but you must
+    distribute all derivative versions as free software under the same
+    terms that I've provided my code to you (i.e. the GNU General Public
+    License). This precludes any use of the code in proprietary or
+    commercial software unless your source code is made freely available.
+    
+    If you wish to use Disulfinder code under a different Open Source 
+    license that's not compatible with the GPL (like the Artistic License, 
+    BSD license, or the Netscape Public License), please contact me
+    (passerini at disi.unitn.it) for permission.
+    
+    This software is distributed in the hope that it will be useful, but
+    WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+    General Public License for more details.
+    
+    You should have received a copy of the GNU General Public License
+    along with this Disulfinder release, in the file LICENSE; if not, 
+    write to the Free Software Foundation, Inc., 51 Franklin St, Fifth
+    Floor, Boston, MA  02110-1301 USA
+
+On Debian systems, the complete text of the GNU General
+Public License can be found in `/usr/share/common-licenses/GPL'.
+
+The Debian packaging is (C) 2009, Laszlo Kajan <lkajan at rostlab.org> and
+is licensed under the GPL, see `/usr/share/common-licenses/GPL'.

Added: trunk/packages/rostlab/disulfinder/trunk/debian/patches/series
===================================================================
Added: trunk/packages/rostlab/disulfinder/trunk/debian/rules
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/rules	                        (rev 0)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/rules	2011-07-09 11:02:11 UTC (rev 7236)
@@ -0,0 +1,91 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+
+
+
+
+configure: configure-stamp
+configure-stamp:
+	dh_testdir
+	# Add here commands to configure the package.
+
+	touch configure-stamp
+
+
+build: build-stamp
+
+build-stamp: configure-stamp  
+	dh_testdir
+
+	# Add here commands to compile the package.
+	$(MAKE) prefix=/usr
+	#docbook-to-man debian/disulfinder.sgml > disulfinder.1
+
+	touch $@
+
+clean: 
+	dh_testdir
+	dh_testroot
+	rm -f build-stamp configure-stamp
+
+	# Add here commands to clean up after the build process.
+	$(MAKE) distclean
+
+	dh_clean 
+
+install: build
+	dh_testdir
+	dh_testroot
+	dh_prep
+	dh_installdirs
+
+	# Add here commands to install the package into debian/disulfinder.
+	$(MAKE) DESTDIR=$(CURDIR)/debian/disulfinder prefix=/usr install
+
+
+# Build architecture-independent files here.
+binary-indep: build install
+# We have nothing to do by default.
+
+# Build architecture-dependent files here.
+binary-arch: build install
+	dh_testdir
+	dh_testroot
+	dh_installchangelogs 
+	dh_installdocs
+	dh_installexamples
+#	dh_install
+#	dh_installmenu
+#	dh_installdebconf	
+#	dh_installlogrotate
+#	dh_installemacsen
+#	dh_installpam
+#	dh_installmime
+#	dh_python
+#	dh_installinit
+#	dh_installcron
+#	dh_installinfo
+	dh_installman
+	dh_link
+	dh_strip
+	dh_compress
+	dh_fixperms
+#	dh_perl
+#	dh_makeshlibs
+	dh_installdeb
+	dh_shlibdeps
+	dh_gencontrol
+	dh_md5sums
+	dh_builddeb
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install configure


Property changes on: trunk/packages/rostlab/disulfinder/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/rostlab/disulfinder/trunk/debian/source/format
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/source/format	                        (rev 0)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/source/format	2011-07-09 11:02:11 UTC (rev 7236)
@@ -0,0 +1 @@
+3.0 (quilt)

Added: trunk/packages/rostlab/disulfinder/trunk/debian/watch
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/watch	                        (rev 0)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/watch	2011-07-09 11:02:11 UTC (rev 7236)
@@ -0,0 +1,2 @@
+version=3
+ftp://rostlab.org/disulfinder/disulfinder-([0-9.]+)\.tar\.gz


