[med-svn] r267 - in trunk/packages/melting/trunk: . debian
Charles Plessy
charles-guest at alioth.debian.org
Thu Apr 12 00:48:58 UTC 2007
Author: charles-guest
Date: 2007-04-12 00:48:58 +0000 (Thu, 12 Apr 2007)
New Revision: 267
Added:
trunk/packages/melting/trunk/debian/
trunk/packages/melting/trunk/debian/changelog
trunk/packages/melting/trunk/debian/compat
trunk/packages/melting/trunk/debian/control
trunk/packages/melting/trunk/debian/copyright
trunk/packages/melting/trunk/debian/melting-gui.desktop
trunk/packages/melting/trunk/debian/melting-gui.manpages
trunk/packages/melting/trunk/debian/melting-gui.menu
trunk/packages/melting/trunk/debian/melting.dirs
trunk/packages/melting/trunk/debian/melting.doc-base
trunk/packages/melting/trunk/debian/melting.docs
trunk/packages/melting/trunk/debian/melting.examples
trunk/packages/melting/trunk/debian/melting.install
trunk/packages/melting/trunk/debian/melting.manpages
trunk/packages/melting/trunk/debian/rules
trunk/packages/melting/trunk/debian/tkmelting.1.xml
trunk/packages/melting/trunk/debian/watch
Log:
[svn-inject] Applying Debian modifications to trunk
Added: trunk/packages/melting/trunk/debian/changelog
===================================================================
--- trunk/packages/melting/trunk/debian/changelog 2007-04-12 00:47:15 UTC (rev 266)
+++ trunk/packages/melting/trunk/debian/changelog 2007-04-12 00:48:58 UTC (rev 267)
@@ -0,0 +1,7 @@
+melting (4.2g-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #418691)
+ * Still full of packaging bugs...
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Thu, 12 Apr 2007 09:40:39 +0900
+
Added: trunk/packages/melting/trunk/debian/compat
===================================================================
--- trunk/packages/melting/trunk/debian/compat 2007-04-12 00:47:15 UTC (rev 266)
+++ trunk/packages/melting/trunk/debian/compat 2007-04-12 00:48:58 UTC (rev 267)
@@ -0,0 +1 @@
+5
Added: trunk/packages/melting/trunk/debian/control
===================================================================
--- trunk/packages/melting/trunk/debian/control 2007-04-12 00:47:15 UTC (rev 266)
+++ trunk/packages/melting/trunk/debian/control 2007-04-12 00:48:58 UTC (rev 267)
@@ -0,0 +1,33 @@
+Source: melting
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Charles Plessy <charles-debian-nospam at plessy.org>
+Build-Depends: debhelper (>= 5)
+Standards-Version: 3.7.2
+XS-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/melting/trunk/
+XS-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/melting
+
+Package: melting
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: melting-gui
+Description: computing 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 easely changed,
+ for instance following an experimental breakthrough. Melting was
+ published in Le Novère N. (2001), Bioinformatics, 17: 1226-1227.
+ .
+ Homepage: http://www.ebi.ac.uk/~lenov/meltinghome.html
+
+Package: melting-gui
+Architecture: all
+Depends: perl-tk, melting
+Description: Graphical user interface for melting
+ This package provide a graphical user interface to the "melting"
+ program.
Added: trunk/packages/melting/trunk/debian/copyright
===================================================================
--- trunk/packages/melting/trunk/debian/copyright 2007-04-12 00:47:15 UTC (rev 266)
+++ trunk/packages/melting/trunk/debian/copyright 2007-04-12 00:48:58 UTC (rev 267)
@@ -0,0 +1,31 @@
+This package was debianized by Charles Plessy
+<charles-debian-nospam at plessy.org> on Wed, 11 Apr 2007 21:19:19 +0900.
+
+Melting was downloaded from http://www.ebi.ac.uk/~lenov/meltinghome.html
+
+Upstream Author: Nicolas Le Novère <lenov at ebi.ac.uk>
+
+Copyright: 1997-2004 Nicolas Le Novère
+
+License:
+
+ 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 can be found in `/usr/share/common-licenses/GPL'.
+
+The Debian packaging is (C) 2007, Charles Plessy
+<charles-debian-nospam at plessy.org>. You can use, redistribute, modify
+the packaging work as if it were in the public domain.
Added: trunk/packages/melting/trunk/debian/melting-gui.desktop
===================================================================
--- trunk/packages/melting/trunk/debian/melting-gui.desktop 2007-04-12 00:47:15 UTC (rev 266)
+++ trunk/packages/melting/trunk/debian/melting-gui.desktop 2007-04-12 00:48:58 UTC (rev 267)
@@ -0,0 +1,17 @@
+[Desktop Entry]
+Version=1.0
+Encoding=UTF-8
+Terminal=false
+Icon=tkmelting
+Exec=tkmelting
+Name=Melting
+GenericName="Oligonucleotide analyser"
+GenericName[en]="Oligonucleotide analyser"
+GenericName[fr]="Analyse d'oligonucléotides"
+GenericName[pt_BR]=""
+Comment="Computes the melting temperature for a nucleic acid duplex."
+Comment[en]="Computes the melting temperature for a nucleic acid duplex."
+Comment[fr]="Calcule la température de fusion d'une paire d'oligonucléotides."
+Comment[pt_BR]=""
+Type=Application
+Categories=Biology;Science;Education;
Added: trunk/packages/melting/trunk/debian/melting-gui.manpages
===================================================================
--- trunk/packages/melting/trunk/debian/melting-gui.manpages 2007-04-12 00:47:15 UTC (rev 266)
+++ trunk/packages/melting/trunk/debian/melting-gui.manpages 2007-04-12 00:48:58 UTC (rev 267)
@@ -0,0 +1 @@
+tkmelting.1
Added: trunk/packages/melting/trunk/debian/melting-gui.menu
===================================================================
--- trunk/packages/melting/trunk/debian/melting-gui.menu 2007-04-12 00:47:15 UTC (rev 266)
+++ trunk/packages/melting/trunk/debian/melting-gui.menu 2007-04-12 00:48:58 UTC (rev 267)
@@ -0,0 +1,7 @@
+?package(melting-gui):\
+ needs="X11"\
+ section="Apps/Science"\
+ title="Melting"\
+ command="/usr/bin/tkmelting.pl"\
+ hints="Primer design"\
+ longtitle="Computes the melting temperature for a nucleic acid duplex."
Added: trunk/packages/melting/trunk/debian/melting.dirs
===================================================================
--- trunk/packages/melting/trunk/debian/melting.dirs 2007-04-12 00:47:15 UTC (rev 266)
+++ trunk/packages/melting/trunk/debian/melting.dirs 2007-04-12 00:48:58 UTC (rev 267)
@@ -0,0 +1,3 @@
+usr/bin
+usr/share/melting
+usr/share/doc/melting
Added: trunk/packages/melting/trunk/debian/melting.doc-base
===================================================================
--- trunk/packages/melting/trunk/debian/melting.doc-base 2007-04-12 00:47:15 UTC (rev 266)
+++ trunk/packages/melting/trunk/debian/melting.doc-base 2007-04-12 00:48:58 UTC (rev 267)
@@ -0,0 +1,16 @@
+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
+
+Format: pdf
+Files: /usr/share/doc/melting/melting.pdf
+
+Format: HTML
+Index: /usr/share/doc/melting/melting/melting.html
+
+
+
Added: trunk/packages/melting/trunk/debian/melting.docs
===================================================================
--- trunk/packages/melting/trunk/debian/melting.docs 2007-04-12 00:47:15 UTC (rev 266)
+++ trunk/packages/melting/trunk/debian/melting.docs 2007-04-12 00:48:58 UTC (rev 267)
@@ -0,0 +1,3 @@
+DOC/melting
+DOC/melting.pdf
+README
Added: trunk/packages/melting/trunk/debian/melting.examples
===================================================================
--- trunk/packages/melting/trunk/debian/melting.examples 2007-04-12 00:47:15 UTC (rev 266)
+++ trunk/packages/melting/trunk/debian/melting.examples 2007-04-12 00:48:58 UTC (rev 267)
@@ -0,0 +1,2 @@
+BIN/multi.pl
+BIN/profil.pl
Added: trunk/packages/melting/trunk/debian/melting.install
===================================================================
--- trunk/packages/melting/trunk/debian/melting.install 2007-04-12 00:47:15 UTC (rev 266)
+++ trunk/packages/melting/trunk/debian/melting.install 2007-04-12 00:48:58 UTC (rev 267)
@@ -0,0 +1,2 @@
+melting usr/bin
+NNFILES usr/share/melting
Added: trunk/packages/melting/trunk/debian/melting.manpages
===================================================================
--- trunk/packages/melting/trunk/debian/melting.manpages 2007-04-12 00:47:15 UTC (rev 266)
+++ trunk/packages/melting/trunk/debian/melting.manpages 2007-04-12 00:48:58 UTC (rev 267)
@@ -0,0 +1 @@
+DOC/melting.1
Added: trunk/packages/melting/trunk/debian/rules
===================================================================
--- trunk/packages/melting/trunk/debian/rules 2007-04-12 00:47:15 UTC (rev 266)
+++ trunk/packages/melting/trunk/debian/rules 2007-04-12 00:48:58 UTC (rev 267)
@@ -0,0 +1,95 @@
+#!/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
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+
+configure: configure-stamp
+configure-stamp:
+ dh_testdir
+ cp makefile.unices Makefile
+ touch configure-stamp
+
+build: build-arch build-indep
+
+build-arch: build-arch-stamp
+build-arch-stamp: configure-stamp
+ $(MAKE)
+ touch build-arch-stamp
+
+build-indep: build-indep-stamp
+build-indep-stamp:
+ xsltproc \
+ -''-nonet \
+ -''-param man.charmap.use.subset "0" \
+ -''-param make.year.ranges "1" \
+ -''-param make.single.year.ranges "1" \
+ debian/tkmelting.1.xml
+ touch build-indep-stamp
+
+clean: configure
+ dh_testdir
+ dh_testroot
+ -$(MAKE) clean
+ rm -f build-arch-stamp build-indep-stamp configure-stamp Makefile tkmelting.1
+ dh_clean
+
+install: install-indep install-arch
+install-indep:
+ dh_testdir
+ dh_testroot
+ dh_clean -k -i
+ dh_installdirs -i
+ dh_install -i
+ install -D BIN/tkmelting.pl $(CURDIR)/debian/melting-gui/usr/bin/tkmelting
+ install -D BIN/melting.hlp $(CURDIR)/debian/melting-gui/usr/share/melting/melting.hlp
+ install -D debian/melting-gui.desktop $(CURDIR)/debian/melting-gui/usr/share/application/melting-gui.desktop
+
+install-arch:
+ dh_testdir
+ dh_testroot
+ dh_clean -k -s
+ dh_installdirs -s
+# install melting $(CURDIR)/debian/melting/usr/bin
+ dh_install -s
+
+binary-common:
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs ChangeLog
+ dh_installdocs
+ dh_installexamples
+ dh_installmenu
+ dh_desktop
+ dh_installman
+# dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+# dh_perl
+ dh_makeshlibs
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+# Build architecture independant packages using the common target.
+binary-indep: build-indep install-indep
+ $(MAKE) -f debian/rules DH_OPTIONS=-i binary-common
+
+# Build architecture dependant packages using the common target.
+binary-arch: build-arch install-arch
+ $(MAKE) -f debian/rules DH_OPTIONS=-s binary-common
+
+binary: binary-arch binary-indep
+.PHONY: build clean binary-indep binary-arch binary install install-indep install-arch configure
Property changes on: trunk/packages/melting/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/melting/trunk/debian/tkmelting.1.xml
===================================================================
--- trunk/packages/melting/trunk/debian/tkmelting.1.xml 2007-04-12 00:47:15 UTC (rev 266)
+++ trunk/packages/melting/trunk/debian/tkmelting.1.xml 2007-04-12 00:48:58 UTC (rev 267)
@@ -0,0 +1,126 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<?xml-stylesheet type="text/xsl"
+ href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
+ "http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd" [
+
+<!-- Process this file with an XSLT processor, e.g. xsltproc: -->
+<!-- `xsltproc \
+ -''-nonet \
+ -''-param man.charmap.use.subset "0" \
+ -''-param make.year.ranges "1" \
+ -''-param make.single.year.ranges "1" \
+ manpage.xml' -->
+
+ <!ENTITY dhfirstname "Charles">
+ <!ENTITY dhsurname "Plessy">
+ <!ENTITY dhemail "charles-debian-nospam at plessy.org">
+ <!ENTITY dhusername "&dhfirstname; &dhsurname;">
+ <!ENTITY dhrelease "0.004">
+ <!-- Please adjust the date whenever revising the manpage. -->
+ <!ENTITY dhdate "2007-04-12">
+ <!ENTITY dhtitle "Melting Manual">
+ <!ENTITY dhucpackage "TKMELTING">
+ <!ENTITY dhpackage "tkmelting">
+ <!ENTITY dhproduct "Melting">
+ <!ENTITY dhsection "1">
+
+]>
+
+<refentry>
+ <refentryinfo>
+ <title>&dhtitle;</title>
+ <productname>&dhpackage;</productname>
+ <releaseinfo role="version">&dhrelease;</releaseinfo>
+ <date>&dhdate;</date>
+ <authorgroup>
+ <author>
+ <firstname>Nicolas</firstname>
+ <surname>Le Novère</surname>
+ <contrib>tkmelting</contrib>
+ <address>
+ <affiliation>
+ <orgname>EMBL-EBI</orgname>
+ </affiliation>
+ <street>Wellcome-Trust Genome Campus Hinxton</street>
+ <city>Cambridge</city>
+ <postcode>CB10 1SD</postcode>
+ <country>UK</country>
+ <email>lenov at ebi.ac.uk</email>
+ </address>
+ </author>
+ <author>
+ <firstname>&dhfirstname;</firstname>
+ <surname>&dhsurname;</surname>
+ <contrib>Wrote and this manpage in DocBook XML for the Debian distribution.</contrib>
+ <address>
+ <email>&dhemail;</email>
+ </address>
+ </author>
+ </authorgroup>
+ <copyright>
+ <year>1996</year>
+ <year>1997</year>
+ <year>1998</year>
+ <year>1999</year>
+ <year>2000</year>
+ <year>2001</year>
+ <year>2002</year>
+ <year>2003</year>
+ <year>2004</year>
+ <year>2005</year>
+ <year>2006</year>
+ <holder>Nicolas le Novère</holder>
+ </copyright>
+ <copyright>
+ <year>2007</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ <legalnotice>
+ <para>
+ Tkmelting 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.
+ </para>
+
+ <para>
+ Tkmelting 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.
+ </para>
+
+ <para>
+ You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ </para>
+
+ <para>
+ On Debian systems, you can find a copy of the GNU General Public License in <filename>/usr/share/common-licences/GPL</filename>. The manpage of tkmelting can be used under the same terms as tkmelting itself.
+ </para>
+ </legalnotice>
+ </refentryinfo>
+
+ <refmeta>
+ <refentrytitle>&dhucpackage;</refentrytitle>
+ <manvolnum>&dhsection;</manvolnum>
+ </refmeta>
+
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+ <refpurpose>Tk interface to MELTING</refpurpose>
+ </refnamediv>
+
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1 id="description">
+ <title>DESCRIPTION</title>
+ <para><command>&dhpackage;</command> starts a graphical user interface to MELTING, a program to calculate for a DNA/DNA, DNA/RNA, and RNA/RNA duplex, the enthalpy, the entropy of the helix-coil transition, and then its melting temperature.</para>
+ </refsect1>
+
+ <refsect1>
+ <title>SEE ALSO</title>
+ <para><citerefentry>
+ <refentrytitle>melting</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>
+ </para>
+ </refsect1>
+</refentry>
Added: trunk/packages/melting/trunk/debian/watch
===================================================================
--- trunk/packages/melting/trunk/debian/watch 2007-04-12 00:47:15 UTC (rev 266)
+++ trunk/packages/melting/trunk/debian/watch 2007-04-12 00:48:58 UTC (rev 267)
@@ -0,0 +1,5 @@
+version=3
+http://www.ebi.ac.uk/~lenov/SOFTWARES/ melting(.*?)_(.*?)\.tar\.gz
+
+
+
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