debian/0000755000000000000000000000000011717740141007171 5ustar debian/watch0000644000000000000000000000006011110210536010201 0ustar version=3 http://sf.net/mipe/ mipe-(.*)\.tar.gz debian/copyright0000644000000000000000000000277711110210536011124 0ustar 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 debian/dirs0000644000000000000000000000003311717736633010064 0ustar usr/bin usr/share/man/man1 debian/changelog0000644000000000000000000000421511717740141011045 0ustar mipe (1.1-4) unstable; urgency=low [ Andreas Tille ] * debian/control: - Fixed Vcs-Fields - Updated Standards-Version to 3.9.2 (no changes needed) - Depends: ${misc:Depends}, ${perl:Depends} * debian/upstream: Added URL * debian/source/format: 3.0 (quilt) * debhelper 8 (control+compat) * debian/rules: rewritten using short dh * debian/install: install *.dtd and *.xsd * debian/manpages: removed because unneeded [ Charles Plessy ] * Documented information in ‘debian/upstream’. * Removed mention of the bibliographic reference in ‘debian/control’. -- Andreas Tille Sat, 18 Feb 2012 16:14:20 +0100 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 A 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 debian/source/0000755000000000000000000000000011717734160010475 5ustar debian/source/format0000644000000000000000000000001411301174376011677 0ustar 3.0 (quilt) debian/compat0000644000000000000000000000000211717734322010373 0ustar 8 debian/install0000644000000000000000000000005211717736612010567 0ustar *.dtd usr/share/mipe *.xsd usr/share/mipe debian/patches/0000755000000000000000000000000011717734114010623 5ustar debian/patches/series0000644000000000000000000000001711717734114012036 0ustar 10_mipe0.patch debian/patches/10_mipe0.patch0000644000000000000000000000375211717734114013165 0ustar 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; debian/rules0000755000000000000000000000104411717736711010260 0ustar #!/usr/bin/make -f # debian/rules for mipe # Copyright 2012 Andreas Tille # see debian/copyright # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 PKG := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p') %: dh $@ override_dh_install: dh_install # remove *.pl extension and create manpages using pod2man for i in *.pl; do \ bname=`echo $$i | sed -e 's/.pl$$//'`; \ cp -a $$i $(CURDIR)/debian/$(PKG)/usr/bin/$$bname ; \ pod2man $$i > $(CURDIR)/debian/$(PKG)/usr/share/man/man1/$${bname}.1 ; \ done debian/control0000644000000000000000000000266211717737406010614 0ustar 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 (>= 8), quilt Standards-Version: 3.9.2 Homepage: http://mipe.sourceforge.net Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mipe/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mipe/trunk/ Package: mipe Architecture: all Depends: libxml-twig-perl, libxml-perl, ${misc:Depends}, ${perl:Depends} 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. debian/docs0000644000000000000000000000000711110210536010024 0ustar README debian/upstream0000644000000000000000000000066711717733764011002 0ustar Archive: SourceForge Contact: Jan Aerts (aerts at users.sourceforge.net) Homepage: http://mipe.sourceforge.net Reference: Author: Aerts J & Veenendaal T. Title: MIPE - a XML-format to facilitate the storage and exchange of PCR-related data Journal: Online Journal of Bioinformatics Number: 2 Volume: 6 Pages: 114-120 Year: 2005 URL: http://users.comcen.com.au/~journals/mipeabs2005.htm Watch: http://sf.net/mipe/ mipe-(.*)\.tar.gz