debian/0000755000000000000000000000000012242342135007164 5ustar debian/control0000644000000000000000000000411112242115254010564 0ustar Source: disulfinder Maintainer: Debian Med Packaging Team Uploaders: Guy Yachdav , Laszlo Kajan , Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9), libboost-dev, libboost-graph-dev, libf2c2-dev Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/rostlab/disulfinder/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/rostlab/disulfinder/trunk/ Homepage: http://disulfind.dsi.unifi.it/ Package: disulfinder Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, disulfinder-data 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. Package: disulfinder-data Architecture: all Depends: ${misc:Depends} Description: data files for predictor of disulfide bonds in proteins 'disulfinder' is for predicting the disulfide bonding state of cysteines and their disulfide connectivity starting from sequence alone. . This package contains all data files to reduce the redundancy between architectures in Debian. debian/disulfinder-data.dirs0000644000000000000000000000002611625520563013273 0ustar usr/share/disulfinder debian/rules0000755000000000000000000000072012242224102010234 0ustar #!/usr/bin/make -f # -*- makefile -*- # Uncomment this to turn on verbose mode. export DH_VERBOSE=1 pkg := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}') pkgdata := $(pkg)-data %: dh $@ override_dh_auto_install: $(MAKE) DESTDIR=$(CURDIR)/debian/$(pkg) prefix=/usr install override_dh_install: dh_install mkdir -p $(CURDIR)/debian/$(pkgdata)/usr/share/$(pkg) mv $(CURDIR)/debian/$(pkg)/usr/share/$(pkg) $(CURDIR)/debian/$(pkgdata)/usr/share/ debian/watch0000644000000000000000000000010711606032463010216 0ustar version=3 ftp://rostlab.org/disulfinder/disulfinder-([0-9.]+)\.tar\.gz debian/upstream0000644000000000000000000000242612214301256010751 0ustar Name: disulfinder Reference: - Author: A. Ceroni and A. Passerini and A. Vullo and P. Frasconi Title: 'DISULFIND: a disulfide bonding state and cysteine connectivity prediction server.' Journal: Nucleic Acids Res Volume: 34 Number: Web Server issue Pages: W177-81 Year: 2006 URL: http://www.ncbi.nlm.nih.gov/pubmed/16844986 PMID: 16844986 - Comment: For the disulphide connectivity predictor Author: Alessandro Vullo and Paolo Frasconi Title: Disulfide connectivity prediction using recursive neural networks and evolutionary information. Journal: Bioinformatics Volume: 20 Number: 5 Pages: 653-9 Year: 2004 Month: March PMID: 15033872 - Comment: For the cystein bonding state predictor Author: A. Ceroni and P. Frasconi and A. Passerini and A. Vullo Title: Predicting the Disulfide Bonding State of Cysteines with Combinations of Kernel Machines Journal: Journal of VLSI Signal Processing Volume: 35 Pages: 287-295 Year: 2003 - Comment: For the cystein bonding state predictor Author: P. Frasconi and A. Passerini and A. Vullo Title: A Two-Stage SVM Architecture for Predicting the Disulfide Bonding State of Cysteines Journal: Proc. IEEE Workshop on Neural Networks for Signal Processing Pages: 25-34 Year: 2002 debian/copyright0000644000000000000000000000415412242201561011120 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Contact: Laszlo Kajan Source: ftp://rostlab.org/disulfinder/ Files: * Copyright: © 2011 Alessio Ceroni, Andrea Passerini , Alessandro Vullo, Paolo Frasconi © 2009 Laszlo Kajan , Technical University Munich (Munich, DE) License: GPL2+ License: GPL2+ 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@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-2'. Files: debian/* Copyright: © 2009-2011 Laszlo Kajan © 2013 Andreas Tille License: GPL2+ debian/source/0000755000000000000000000000000011627676470010506 5ustar debian/source/format0000644000000000000000000000001411606032463011675 0ustar 3.0 (quilt) debian/changelog0000644000000000000000000000330012242342135011032 0ustar disulfinder (1.2.11-3) unstable; urgency=low * debian/upstream: Valid BibTeX syntax in author strings * debian/control: - cme fix dpkg-control - Priority: s/extra/optional/ - canonical Vcs URLs - debhelper 9 * debian/copyright: DEP5 * debian/patches/hardening.patch: Propagate hardening options * debian/rules: use dh consequently * README.Debian: references are now in debian/upstream - install this instead into doc directory -- Andreas Tille Sun, 17 Nov 2013 08:46:05 +0100 disulfinder (1.2.11-2) unstable; urgency=low * added mkdir debian/disulfinder-data/usr/share/disulfinder/ to debian/rules before moving Models to disulfinder-data package to resolve building issue on certain architectures (Closes: #639571) -- Laszlo Kajan Wed, 31 Aug 2011 20:47:26 +0200 disulfinder (1.2.11-1) unstable; urgency=low * New upstream release -- Laszlo Kajan Fri, 26 Aug 2011 13:02:59 +0200 disulfinder (1.2.10-1) unstable; urgency=low * New upstream release * The new upstream contains a rewritten version of require.h: the new require.h is no longer based on any code with restricted license, it is released under the GPL (see source) [Steffen] * moved to dh7 * added data package -- Laszlo Kajan Thu, 18 Aug 2011 11:28:02 +0200 disulfinder (1.2.9-2) UNRELEASED; urgency=low [Steffen] * Added build-arch/-indep targets to help lintian -- Laszlo Kajan Sun, 24 Jul 2011 15:51:08 +0200 disulfinder (1.2.9-1) unstable; urgency=low * Initial release (Closes: #634177) -- Laszlo Kajan Sat, 09 Jul 2011 11:54:46 +0200 debian/patches/0000755000000000000000000000000012242202437010613 5ustar debian/patches/hardening.patch0000644000000000000000000000114312242202437013572 0ustar Author: Andreas Tille LastChanged: Sun, 17 Nov 2013 08:46:05 +0100 Description: Propagate hardening options --- a/Makefile +++ b/Makefile @@ -13,7 +13,7 @@ MAN1PAGES := disulfinder.1 prefix := /usr docdir := $(prefix)/share/doc/$(PACKAGE) -CXXFLAGS := -DDEFAULT_PKGDATADIR=\"$(prefix)/share/disulfinder\" +CXXFLAGS += -DDEFAULT_PKGDATADIR=\"$(prefix)/share/disulfinder\" export CXXFLAGS .PHONY: all --- a/disulfind/src/Makefile +++ b/disulfind/src/Makefile @@ -1,5 +1,5 @@ LIBS=-lCommon -LDFLAGS=-LCommon/ +LDFLAGS+=-LCommon/ TARGETS=disulfinder disultrainer ifndef CXX CXX=g++ debian/patches/series0000644000000000000000000000002012242202277012022 0ustar hardening.patch debian/compat0000644000000000000000000000000212242115217010361 0ustar 9 debian/docs0000644000000000000000000000002012242342066010032 0ustar debian/upstream