debian/0000755000000000000000000000000012201674421007165 5ustar debian/melting.examples0000644000000000000000000000003711110210276012354 0ustar BIN/multi.pl BIN/profil.pl TESTdebian/README.Debian0000644000000000000000000000117711301521375011233 0ustar Meting for Debian ───────────────── Notes about how this package was tested: After building locally on the developper’s computer, the programs melting and tkmelting were briefly tested before uploading the package to the Debian archive. - melting was ran with the following command line: melting -SAAAAAAAAAAAAAAA -HA -k0.01 -P0.01 - The tkmelting interface was invoked from the Gnome menu, and the meltin temperature of 0.01 M of the AAAAAAAAAAAAAAA oligonucleotide was calculated for a 0.01 M salt concentration. -- Charles Plessy Fri, 20 Nov 2009 10:00:28 +0900 debian/melting.dirs0000644000000000000000000000006011110210276011473 0ustar usr/bin usr/share/melting usr/share/doc/melting debian/source/0000755000000000000000000000000012201660142010460 5ustar debian/source/format0000644000000000000000000000001411520325247011675 0ustar 3.0 (quilt) debian/README.source0000644000000000000000000000026711260647760011363 0ustar This packages uses the quilt patch system. Please read /usr/share/doc/quilt/README.source for more information. -- Andreas Tille Wed, 30 Sep 2009 14:31:20 +0200 debian/copyright0000644000000000000000000000277112201661322011123 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: Melting Upstream-Contact: Nicolas Le Novère Marine Dumousseau Source: http://sourceforge.net/projects/melting/files/meltingC/melting4_3/ Files-Excluded: BIN/melting4_3* svn-commit.tmp Files: * Copyright: 1997–2009, Nicolas Le Novère 1997–2009, Marine Dumousseau License: GPL-2+ Files: debian/* Copyright: 2007–2009 Charles Plessy 2008-2012 Andreas Tille 2008 David Paleino License: GPL-2+ License: GPL-2+ Melting 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. . Melting 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 package; 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 version 2 can be found in ‘/usr/share/common-licenses/GPL-2’. debian/upstream0000644000000000000000000000120711736613315010757 0ustar Contact: Nicolas Le Novère Homepage: http://www.ebi.ac.uk/compneur-srv/melting/ Name: MELTING Reference: author: Le Novère, Nicolas title: MELTING, computing the melting temperature of nucleic acid duplex journal: Bioinformatics volume: 17 number: 12 pages: 1226-1227 year: 2001 DOI: 10.1093/bioinformatics/17.12.1226 PMID: 11751232 URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/17/12/1226 eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/17/12/1226.pdf Screenshot: http://www.ebi.ac.uk/compneur-srv/melting/melting.jpg Webservice: http://www.ebi.ac.uk/compneur-srv/melting/melt.php debian/rules0000755000000000000000000000206412201661462010250 0ustar #!/usr/bin/make -f # -*- makefile -*- # Build rules for melting. you can use this file without restriction. # This has to be exported to make some magic below work. export DH_OPTIONS %: dh $@ override_dh_auto_build: $(MAKE) -f makefile.unices NNDIR=/usr/share/melting/NNFILES override_dh_clean: dh_clean melting.o decode.o calcul.o melting override_dh_install: dh_install install -D BIN/tkmelting.pl $(CURDIR)/debian/melting-gui/usr/bin/tkmelting install -m 644 -D BIN/melting.hlp $(CURDIR)/debian/melting-gui/usr/share/melting/melting.hlp install -m 644 -D melting-gui.desktop $(CURDIR)/debian/melting-gui/usr/share/applications/melting-gui.desktop # Remark: The following uscan command requires devscripts > 2.12.4 which is not # yet released at the time of this package release. The code can be obtained # via # git clone git://tille@git.debian.org/git/users/tille/devscripts.git # and then use scripts/uscan.pl get-orig-source: mkdir -p ../tarballs uscan --verbose --force-download --destdir=../tarballs --repack-compression xz debian/melting-gui.manpages0000644000000000000000000000002011211672053013112 0ustar DOC/tkmelting.1 debian/melting.docs0000644000000000000000000000006411211672053011475 0ustar DOC/melting DOC/melting.html DOC/melting.pdf README debian/patches/0000755000000000000000000000000012201675305010616 5ustar debian/patches/tkmelting.patch0000644000000000000000000000161112201660246013632 0ustar Author: Charles Plessy Description: Find perl in /usr/bin, and use a different hardcoded path to the help. Forwarded: not yet. License: same as Melting itself. --- a/BIN/tkmelting.pl +++ b/BIN/tkmelting.pl @@ -1,4 +1,5 @@ -eval '(exit $?0)' && eval 'exec perl -S $0 ${1+ "$@"}' && eval 'exec perl -S $0 $argv:q' if 0; +#!/usr/bin/perl +#eval '(exit $?0)' && eval 'exec perl -S $0 ${1+ "$@"}' && eval 'exec perl -S $0 $argv:q' if 0; ############################################################################## # MELTING # @@ -455,7 +456,7 @@ sub show_help{ )->pack(-expand => 1, -fill => 'both' ); - open(FH,"melting.hlp") || die "unable to open melting.hlp"; + open(FH,"/usr/share/melting/melting.hlp") || die "unable to open melting.hlp"; while (){ $helpText->insert('end', $_); } debian/patches/20_fix_manpage.patch0000644000000000000000000000047312201660251014414 0ustar Author: Andreas Tille Description: Fix typo in manpage --- a/DOC/melting.1 +++ b/DOC/melting.1 @@ -60,7 +60,7 @@ distribution of melting provides some fi (SantaLucia et al 1996), .I sug96a.nn (Sugimoto et al 1996) -.Isan04a.nn +.I san04a.nn (Santalucia et al 2004) (DNA/DNA), .I fre86a.nn debian/patches/hardening.patch0000644000000000000000000000135312201675305013600 0ustar Description: Enable propagation of hardening flags Author: Andreas Tille Date: Sun, 11 Aug 2013 11:51:52 +0200 --- a/makefile.unices +++ b/makefile.unices @@ -47,14 +47,14 @@ VPATH = $(srcdir) # Here add your compiler name and the chosen options CC = gcc # options to produce the release version -CFLAGS = -Wall -pedantic -O3 -DNN_BASE=\"$(NNDIR)\" +CFLAGS += -Wall -pedantic -O3 -DNN_BASE=\"$(NNDIR)\" # options to produce a version to debug and prof #CFLAGS = -Wall -pedantic -g -DNN_BASE=\"$(NNDIR)\" OBJECTS = melting.o decode.o calcul.o all : $(OBJECTS) - $(CC) $(CFLAGS) -o melting $(OBJECTS) -lm + $(CC) $(CFLAGS) -o melting $(OBJECTS) $(LDFLAGS) -lm $(OBJECTS) : common.h melting.o : melting.c melting.h debian/patches/series0000644000000000000000000000006512201674221012030 0ustar tkmelting.patch 20_fix_manpage.patch hardening.patch debian/melting-gui.menu0000644000000000000000000000034111110210276012262 0ustar ?package(melting-gui):\ needs="X11"\ section="Applications/Science/Biology"\ title="Melting"\ command="/usr/bin/tkmelting"\ hints="Primer design"\ longtitle="Computes the melting temperature for a nucleic acid duplex." debian/melting.install0000644000000000000000000000015111263031216012205 0ustar melting usr/bin NNFILES usr/share/melting BIN/multi.pl usr/share/melting BIN/profil.pl usr/share/melting debian/melting.doc-base0000644000000000000000000000070011211672053012217 0ustar Document: melting Title: The melting Manual Author: Nicolas Le Novère Abstract: This manual describes what melting is and how it can be used to compute, for a nucleic acid duplex, the enthalpy, the entropy and the melting temperature of the helix-coil transitions. Section: Science/Biology Format: pdf Files: /usr/share/doc/melting/melting.pdf.gz Format: HTML Index: /usr/share/doc/melting/melting.html Files: /usr/share/doc/melting/melting/* debian/watch0000644000000000000000000000036212201673356010225 0ustar version=3 opts=uversionmangle=s/_/\./g,dversionmangle=s/\+dfsg//g \ http://sf.net/melting/melting(\d.+)\.tar\.gz # MELTING5 is some kind of different program #opts="uversionmangle=s/_/\./" \ # http://sf.net/melting/MELTING([\d._]*)\.tar\.gz debian/changelog0000644000000000000000000001132512201674421011041 0ustar melting (4.3.1+dfsg-1) unstable; urgency=low [ Thorsten Alteholz ] * new upstream version * debian/watch: new syntax * debian/control: bump standard to 3.9.4 (no changes) [ Andreas Tille ] * debian/control: - cme fix dpkg-control - anonscm for Vcs fields * debian/copyright: Add Files-Excluded * debian/watch: handle +dfsg suffix * debian/patch/hardening.patch: propagate hardening options -- Andreas Tille Sun, 11 Aug 2013 11:51:52 +0200 melting (4.3c-2) unstable; urgency=low [ Charles Plessy ] * renamed debian/upstream-metadata.yaml to debian/upstream * debian/source/format: 3.0 (quilt) * debian/upstream: Moved DOI+PMID to references * debian/control: - Standards-Version: 3.9.3 (no changes needed) - Fixed Vcs fields * debian/changelog: Fixed DEP5 and verified using cme fix dpkg-copyright * debian/references: removed because content is now in debian/upstream * debhelper 9 (control+compat) * debian/rules: rewritten to use short dh -- Andreas Tille Tue, 03 Apr 2012 17:27:35 +0200 melting (4.3c-1) unstable; urgency=low * New upstream release: calls melting from the PATH with its base name (Closes: #549881). * debian/melting/install: multi.pl and profil.pl available in /usr/share/melting. * debian/copyright refreshed to latest experimentations on the format. * Target generating tkmelting manpage removed from debian/rules. * Added various informations about upstream in debian/upstream-metadata.yaml. * Document how to test melting and tkmelting in debian/README.Debian. -- Charles Plessy Fri, 20 Nov 2009 10:00:28 +0900 melting (4.3b-1) unstable; urgency=low Tkmelting did not work in my tests. * New upstream release, with new options for Tris, potassium and magnesium concentrations, as well as support for inosine bases. [ Charles Plessy ] * debian/control: - Moved bibliographic reference from the long description to a BibTeX file (debian/reference, installed in /usr/share/doc/melting/reference). - Incremented Standards-Version to reflect conformance with Policy 3.8.1 (no changes needed). - Improved the description of melting-gui (Closes: #528999). - Dropped versionned build-dependency on quilt (satisfied even in oldstable). - Build-Depend on dephelper 7 (debian/compat set to 7). * debian/rules - NNDIR=/usr/share/melting/NNFILES passed as a make argument instead of through a patch (debian/patches/makefile.patch deleted). - clean target rewritten so that debian/patches/makefile-clean.patch could be deleted. - Use ‘dh’ in binary-arch and binary-indep targets. * Deleted debian/patches/melting.c_silent.patch and debian/patches/melting.1_escape.patch cosmetic deviations from Upstream. * debian/copyright updated and converted to latest version of the machine-readable format. * debian/tkmelting.1* and debian/melting-gui.desktop were adopted upstream and deleted from the debian directory. [ David Paleino ] * Removed myself from Uploaders [ Andreas Tille ] * debian/control: - Standards-Version: 3.8.3 (Added README.Source) - s/Debian-Med/Debian Med/ * debian/patches/20_fix_manpage.patch: Fix typo in manpage -- Andreas Tille Wed, 30 Sep 2009 14:31:20 +0200 melting (4.2h-3) unstable; urgency=low * Changed the doc-base section according to the new policy. * Updated my email address. -- Charles Plessy Sun, 06 Jul 2008 18:11:48 +0900 melting (4.2h-2) unstable; urgency=low [ Charles Plessy ] * Moved the Homepage: field out from the package's description. * Debian menu transition: updated debian/melting.doc-base. [ David Paleino ] * debian/tkmeltin.1 added - statically built * debian/control: - B-D updated (see above) - added myself to Uploaders - moved XS-Vcs-* to Vcs-* * debian/rules: - manpage statically built - minor changes * Updated to Standards-Version 3.7.3 (no changes needed) [ Andreas Tille ] * Added myself to uploaders * debian/melting-gui.manpages: Fixed path to man page * debian/melting.doc-base: Removed extra whitespace -- Andreas Tille Tue, 18 Mar 2008 10:32:48 +0100 melting (4.2h-1) unstable; urgency=low * New upstream version: switch to UTF-8 encoding. * Corrects a typo in package description (Closes: #422983). * Debian Menu transition: Apps/Science becomes Applications/Science/Biology. -- Charles Plessy Mon, 20 Aug 2007 23:45:32 +0900 melting (4.2g-1) unstable; urgency=low * Initial release (Closes: #418691) -- Charles Plessy Sun, 22 Apr 2007 11:49:38 +0900 debian/melting.manpages0000644000000000000000000000001611110210276012326 0ustar DOC/melting.1 debian/compat0000644000000000000000000000000211736616066010400 0ustar 9 debian/control0000644000000000000000000000316512201660030010564 0ustar Source: melting Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Thorsten Alteholz Section: science Priority: optional Build-Depends: debhelper (>= 9) Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/melting/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/melting/trunk/ Homepage: http://www.ebi.ac.uk/compneur-srv/melting/ Package: melting Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: melting-gui Description: compute the melting temperature of nucleic acid duplex This program computes, for a nucleic acid duplex, the enthalpy, the entropy and the melting temperature of the helix-coil transitions. Three types of hybridisation are possible: DNA/DNA, DNA/RNA, and RNA/RNA. The program first computes the hybridisation enthalpy and entropy from the elementary parameters of each Crick's pair by the nearest-neighbor method. Then the melting temperature is computed. The set of thermodynamic parameters can be easily changed, for instance following an experimental breakthrough. Package: melting-gui Architecture: all Depends: perl-tk, melting, ${misc:Depends} Description: graphical interface to compute the melting temperature of nucleic acid duplex This package provides a graphical user interface for the “melting” program, which computes for a nucleic acid duplex the enthalpy, the entropy and the melting temperature of the helix-coil transitions.