--- mipe-1.1.orig/debian/manpages +++ mipe-1.1/debian/manpages @@ -0,0 +1,22 @@ +csv2mipe.1 +genotype2mipe.1 +mipe06to07.1 +mipe08to09.1 +mipe0_9to1_0.1 +mipe2dbSTS.1 +mipe2fas.1 +mipe2genotypes.1 +mipe2html.1 +mipe2pcroverview.1 +mipe2pcrprimers.1 +mipe2putativesbeprimers.1 +mipe2sbeprimers.1 +mipe2snps.1 +mipeCheckSanity.1 +removePcrFromMipe.1 +removeSbeFromMipe.1 +removeSnpFromMipe.1 +sbe2mipe.1 +snp2mipe.1 +snpPosOnDesign.1 +snpPosOnSource.1 --- mipe-1.1.orig/debian/dirs +++ mipe-1.1/debian/dirs @@ -0,0 +1,2 @@ +usr/bin +usr/share/mipe --- mipe-1.1.orig/debian/copyright +++ mipe-1.1/debian/copyright @@ -0,0 +1,31 @@ +Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=130 +Upstream-Author: Jan Aerts (aerts at users.sourceforge.net) +Packaged-By: Steffen Moeller , + Andreas Tille +Packaged-Date: Wed, 20 Jul 2005 13:30:13 +0200 +Original-Source-Location: http://downloads.sourceforge.net/mipe/mipe-1.1.tar.gz + +Files: * +Copyright: © 2003-2005 Jan Aerts +License: LGPL-2.1+ + This library is free software; you can redistribute it and/or + modify it under the terms of the GNU Lesser General Public + License as published by the Free Software Foundation; either + version 2.1 of the License, or (at your option) any later version. + . + This library 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 + Lesser General Public License for more details. + . + You should have received a copy of the GNU Lesser General Public + License along with this library ('COPYING'); if not, write to the Free Software + Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA +X-Comment: On Debian systems, the complete text of the GNU Lesser + General Public License can be found in `/usr/share/common-licenses/LGPL'. + +Files: debian/* +Copyright: © 2003—2008 Steffen Moeller + © 2003—2008 Andreas Tille + © 2008 Charles Plessy +License: Same as MIPE itself --- mipe-1.1.orig/debian/watch +++ mipe-1.1/debian/watch @@ -0,0 +1,2 @@ +version=3 +http://sf.net/mipe/ mipe-(.*)\.tar.gz --- mipe-1.1.orig/debian/rules +++ mipe-1.1/debian/rules @@ -0,0 +1,81 @@ +#!/usr/bin/make -f +# debian/rules for clustalw-mpi +# Copyright 2004-2008 Steffen Moeller, Andreas Tille +# see debian/copyright + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +include /usr/share/quilt/quilt.make + +.SUFFIXES: .pl .1 + +%.1: %.pl + pod2man $< > $@ + +SOURCES=csv2mipe.pl genotype2mipe.pl mipe06to07.pl mipe08to09.pl \ + mipe0_9to1_0.pl mipe2dbSTS.pl mipe2fas.pl mipe2genotypes.pl mipe2html.pl \ + mipe2pcroverview.pl mipe2pcrprimers.pl mipe2putativesbeprimers.pl mipe2sbeprimers.pl \ + mipe2snps.pl mipeCheckSanity.pl removePcrFromMipe.pl removeSbeFromMipe.pl \ + removeSnpFromMipe.pl sbe2mipe.pl snp2mipe.pl snpPosOnDesign.pl snpPosOnSource.pl + +MANPAGES=csv2mipe.1 genotype2mipe.1 mipe06to07.1 mipe08to09.1 \ + mipe0_9to1_0.1 mipe2dbSTS.1 mipe2fas.1 mipe2genotypes.1 mipe2html.1 \ + mipe2pcroverview.1 mipe2pcrprimers.1 mipe2putativesbeprimers.1 mipe2sbeprimers.1 \ + mipe2snps.1 mipeCheckSanity.1 removePcrFromMipe.1 removeSbeFromMipe.1 \ + removeSnpFromMipe.1 sbe2mipe.1 snp2mipe.1 snpPosOnDesign.1 snpPosOnSource.1 + +CFLAGS = -Wall -g + +ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS))) + CFLAGS += -O0 +else + CFLAGS += -O2 +endif + +configure: + +build: patch $(MANPAGES) + +clean: unpatch + dh_testdir + dh_testroot + rm -f build-stamp configure-stamp + dh_clean *.1 + +install: build + dh_testdir + dh_testroot + dh_clean -k + dh_installdirs + + # Add here commands to install the package into debian/mipe. + cp *.dtd *.xsd $(CURDIR)/debian/mipe/usr/share/mipe/ + for i in *.pl; do \ + bname=`echo $$i | sed -e 's/.pl$$//'`; \ + cp $$i $(CURDIR)/debian/mipe/usr/bin/$$bname ; \ + done + +# Build architecture-dependent files here. +binary-arch: build install +# We have nothing to do by default. + +# Build architecture-independent files here. +binary-indep: build install + dh_testdir + dh_testroot + dh_installchangelogs + dh_installdocs + dh_installexamples + dh_installman + dh_compress + dh_fixperms + dh_perl + 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 --- mipe-1.1.orig/debian/control +++ mipe-1.1/debian/control @@ -0,0 +1,36 @@ +Source: mipe +Section: science +Priority: optional +Maintainer: Debian-Med Packaging Team +DM-Upload-Allowed: yes +Uploaders: Steffen Moeller , + Andreas Tille , + Charles Plessy +Build-Depends-Indep: perl +Build-Depends: debhelper (>= 5.0), quilt +Standards-Version: 3.7.3 +Homepage: http://mipe.sourceforge.net +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mipe/trunk/?rev=0&sc=0 +Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mipe/trunk/ + +Package: mipe +Architecture: all +Depends: libxml-twig-perl, libxml-perl +Description: Tools to store PCR-derived data + MIPE provides a standard format to exchange and/or storage of all + information associated with PCR experiments using a flat text file. This will: + * allow for exchange of PCR data between researchers/laboratories + * enable traceability of the data + * prevent problems when submitting data to dbSTS or dbSNP + * enable the writing of standard scripts to extract data (e.g. a + list of PCR primers, SNP positions or haplotypes for different animals) + . + Although this tool can be used for data storage, it's primary focus + should be data exchange. For larger repositories, relational databases + are more appropriate for storage of these data. The MIPE format could + then be used as a standard format to import into and/or export from + these databases. + . + MIPE was published in: Aerts J & Veenendaal T. MIPE - a XML-format to + facilitate the storage and exchange of PCR-related data. Online Journal of + Bioinformatics 6(2): 114-120 (2005). --- mipe-1.1.orig/debian/docs +++ mipe-1.1/debian/docs @@ -0,0 +1 @@ +README --- mipe-1.1.orig/debian/compat +++ mipe-1.1/debian/compat @@ -0,0 +1 @@ +5 --- mipe-1.1.orig/debian/changelog +++ mipe-1.1/debian/changelog @@ -0,0 +1,43 @@ +mipe (1.1-3) unstable; urgency=low + + * debian/control: + - Corrected typo in long description (Closes: #458400). + - Dropped unnecessary dependency on libcgi-perl (Closes: #485011). + - Added a reference to the MIPE publication. + - Listed myself in the `Uploaders:' field. + * debian/watch: repaired (Closes: #449990). + * debian/copyright: + - Lifted to revision 130 of the machine-readable format draft; + - relicenced the packaging work to "same as MIPE itself", with + the agreement of Andreas and Steffen; + - added myself to the Hall of Fame. + * debian/patches/10_mipe0.patch improved and forwarded upstream. + + -- Charles Plessy Sun, 15 Jun 2008 15:39:13 +0900 + +mipe (1.1-2) unstable; urgency=low + + [ Andreas Tille ] + * Group maintenance by Debian-Med team + - XS-DM-Upload-Allowed: Yes + - Vcs tags + - Use correct address as Uploader: Steffen Moeller + * Removed [Biology] from short description + * Moved Homepage from long description to control fields + * Standards-Version: 3.7.3 (no changes needed) + * debhelper >= 5 + * Patches using quilt + * debian/copyright machine readable + + [ Charles Plessy ] + * debian/watch uses the sf.net redirector instead of p.d.o/~lolando. + + -- Andreas Tille Mon, 07 Apr 2008 10:52:32 +0200 + +mipe (1.1-1) unstable; urgency=low + + * Initial release (Closes:Bug#319330). + * Kindly sponsored by Andreas Tille. + + -- Steffen Moeller Wed, 20 Jul 2005 13:30:13 +0200 + --- mipe-1.1.orig/debian/patches/series +++ mipe-1.1/debian/patches/series @@ -0,0 +1 @@ +10_mipe0.patch --- mipe-1.1.orig/debian/patches/10_mipe0.patch +++ mipe-1.1/debian/patches/10_mipe0.patch @@ -0,0 +1,88 @@ +Authors: Andreas Tille and Steffen Möller +Forwarded: http://sourceforge.net/tracker/index.php?func=detail&aid=1994235&group_id=109419&atid=653428 +Description: This patch adds missing manpages to some MIPE scripts, via their + POD documentation. +License: Same as MIPE itself. +--- mipe-1.1.orig/mipe06to07.pl ++++ mipe-1.1/mipe06to07.pl +@@ -14,6 +14,24 @@ + # License along with this library ('COPYING'); if not, write to the Free Software + # Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA + ++=head1 NAME ++ ++mipe06to07 - Reads a MIPE file version 0.6 and prints it in version 0.7 ++ ++=head1 SYNOPSIS ++ ++mipe06to07 yourfile-in-version-0.6.mipe ++ ++=head1 ADDITIONAL INFO ++ ++See http://mipe.sourceforge.net ++ ++=head1 AUTHOR ++ ++Jan Aerts (jan.aerts@bbsrc.ac.uk) ++ ++=cut ++ + use strict; + use warnings; + use XML::Twig; +--- mipe-1.1.orig/mipe08to09.pl ++++ mipe-1.1/mipe08to09.pl +@@ -14,6 +14,25 @@ + # License along with this library ('COPYING'); if not, write to the Free Software + # Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA + ++=head1 NAME ++ ++mipe08to09 - Reads a MIPE file version 0.8 and prints it in version 0.9 ++ ++=head1 SYNOPSIS ++ ++mipe08to09 yourfile-in-version-0.8.mipe ++ ++=head1 ADDITIONAL INFO ++ ++See http://mipe.sourceforge.net ++ ++=head1 AUTHOR ++ ++Jan Aerts (jan.aerts@bbsrc.ac.uk) ++ ++=cut ++ ++ + use strict; + use warnings; + use XML::Twig; +--- mipe-1.1.orig/mipe0_9to1_0.pl ++++ mipe-1.1/mipe0_9to1_0.pl +@@ -14,6 +14,25 @@ + # License along with this library ('COPYING'); if not, write to the Free Software + # Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA + ++=head1 NAME ++ ++mipe0_9to1_0 - Reads a MIPE file version 0.9 and prints it in version 1.0 ++ ++=head1 SYNOPSIS ++ ++mipe0_9to1_0 yourfile-in-version-0.9.mipe ++ ++=head1 ADDITIONAL INFO ++ ++See http://mipe.sourceforge.net ++ ++=head1 AUTHOR ++ ++Jan Aerts (jan.aerts@bbsrc.ac.uk) ++ ++=cut ++ ++ + use strict; + use warnings; + use XML::Twig;