[med-svn] r1692 - in trunk/packages: . mipe mipe/trunk mipe/trunk/debian mipe/trunk/debian/patches
tille at alioth.debian.org
tille at alioth.debian.org
Mon Apr 7 08:45:20 UTC 2008
Author: tille
Date: 2008-04-07 08:45:20 +0000 (Mon, 07 Apr 2008)
New Revision: 1692
Added:
trunk/packages/mipe/
trunk/packages/mipe/tags/
trunk/packages/mipe/trunk/
trunk/packages/mipe/trunk/debian/
trunk/packages/mipe/trunk/debian/changelog
trunk/packages/mipe/trunk/debian/compat
trunk/packages/mipe/trunk/debian/control
trunk/packages/mipe/trunk/debian/copyright
trunk/packages/mipe/trunk/debian/dirs
trunk/packages/mipe/trunk/debian/docs
trunk/packages/mipe/trunk/debian/manpages
trunk/packages/mipe/trunk/debian/patches/
trunk/packages/mipe/trunk/debian/patches/10_mipe0.patch
trunk/packages/mipe/trunk/debian/patches/series
trunk/packages/mipe/trunk/debian/rules
trunk/packages/mipe/trunk/debian/watch
Log:
Initial commit with patches implemented in quilt
Added: trunk/packages/mipe/trunk/debian/changelog
===================================================================
--- trunk/packages/mipe/trunk/debian/changelog (rev 0)
+++ trunk/packages/mipe/trunk/debian/changelog 2008-04-07 08:45:20 UTC (rev 1692)
@@ -0,0 +1,7 @@
+mipe (1.1-1) unstable; urgency=low
+
+ * Initial release (Closes:Bug#319330).
+ * Kindly sponsored by Andreas Tille.
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Wed, 20 Jul 2005 13:30:13 +0200
+
Added: trunk/packages/mipe/trunk/debian/compat
===================================================================
--- trunk/packages/mipe/trunk/debian/compat (rev 0)
+++ trunk/packages/mipe/trunk/debian/compat 2008-04-07 08:45:20 UTC (rev 1692)
@@ -0,0 +1 @@
+4
Added: trunk/packages/mipe/trunk/debian/control
===================================================================
--- trunk/packages/mipe/trunk/debian/control (rev 0)
+++ trunk/packages/mipe/trunk/debian/control 2008-04-07 08:45:20 UTC (rev 1692)
@@ -0,0 +1,26 @@
+Source: mipe
+Section: science
+Priority: optional
+Maintainer: Steffen Moeller <moeller at pzr.uni-rostock.de>
+Build-Depends-Indep: debhelper (>= 4.0.0), perl
+Standards-Version: 3.6.2.1
+
+Package: mipe
+Architecture: all
+Depends: libxml-twig-perl, libcgi-perl, libxml-perl
+Description: [Biology] 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 reporisitories, 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.
+ .
+ Homepage: http://mipe.sourceforge.net
Added: trunk/packages/mipe/trunk/debian/copyright
===================================================================
--- trunk/packages/mipe/trunk/debian/copyright (rev 0)
+++ trunk/packages/mipe/trunk/debian/copyright 2008-04-07 08:45:20 UTC (rev 1692)
@@ -0,0 +1,26 @@
+This package was debianized by Steffen Moeller <moeller at pzr.uni-rostock.de> on
+Wed, 20 Jul 2005 13:30:13 +0200.
+
+It was downloaded from http://sourceforge.net/projects/mipe
+
+Copyright Holder: Jan Aerts <jan.aerts at bbsrc.ac.uk>
+
+License:
+
+ This package 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 of the License, or (at your option) any later version.
+
+ This package 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 package; if not, write to the Free Software
+ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+
+On Debian systems, the complete text of the GNU Lesser General
+Public License can be found in `/usr/share/common-licenses/LGPL'.
+
Added: trunk/packages/mipe/trunk/debian/dirs
===================================================================
--- trunk/packages/mipe/trunk/debian/dirs (rev 0)
+++ trunk/packages/mipe/trunk/debian/dirs 2008-04-07 08:45:20 UTC (rev 1692)
@@ -0,0 +1,2 @@
+usr/bin
+usr/share/mipe
Added: trunk/packages/mipe/trunk/debian/docs
===================================================================
--- trunk/packages/mipe/trunk/debian/docs (rev 0)
+++ trunk/packages/mipe/trunk/debian/docs 2008-04-07 08:45:20 UTC (rev 1692)
@@ -0,0 +1 @@
+README
Added: trunk/packages/mipe/trunk/debian/manpages
===================================================================
--- trunk/packages/mipe/trunk/debian/manpages (rev 0)
+++ trunk/packages/mipe/trunk/debian/manpages 2008-04-07 08:45:20 UTC (rev 1692)
@@ -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
Added: trunk/packages/mipe/trunk/debian/patches/10_mipe0.patch
===================================================================
--- trunk/packages/mipe/trunk/debian/patches/10_mipe0.patch (rev 0)
+++ trunk/packages/mipe/trunk/debian/patches/10_mipe0.patch 2008-04-07 08:45:20 UTC (rev 1692)
@@ -0,0 +1,83 @@
+--- 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 - unknown function, based on MIPE version v1.1
++
++=head1 SYNOPSIS
++
++This head was given only as a stub to make lintian happy and as a reminder for Jan to describe this file.
++
++=head1 ADDITIONAL INFO
++
++See http://mipe.sourceforge.net
++
++=head1 AUTHOR
++
++Jan Aerts (jan.aerts at 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 - unknown function, based on MIPE version v1.1
++
++=head1 SYNOPSIS
++
++This head was given only as a stub to make lintian happy and as a reminder for Jan to describe this file.
++
++=head1 ADDITIONAL INFO
++
++See http://mipe.sourceforge.net
++
++=head1 AUTHOR
++
++Jan Aerts (jan.aerts at 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 - unknown function, based on MIPE version v1.1
++
++=head1 SYNOPSIS
++
++This head was given only as a stub to make lintian happy and as a reminder for Jan to describe this file.
++
++=head1 ADDITIONAL INFO
++
++See http://mipe.sourceforge.net
++
++=head1 AUTHOR
++
++Jan Aerts (jan.aerts at bbsrc.ac.uk)
++
++=cut
++
++
+ use strict;
+ use warnings;
+ use XML::Twig;
Added: trunk/packages/mipe/trunk/debian/patches/series
===================================================================
--- trunk/packages/mipe/trunk/debian/patches/series (rev 0)
+++ trunk/packages/mipe/trunk/debian/patches/series 2008-04-07 08:45:20 UTC (rev 1692)
@@ -0,0 +1 @@
+10_mipe0.patch
Added: trunk/packages/mipe/trunk/debian/rules
===================================================================
--- trunk/packages/mipe/trunk/debian/rules (rev 0)
+++ trunk/packages/mipe/trunk/debian/rules 2008-04-07 08:45:20 UTC (rev 1692)
@@ -0,0 +1,82 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+.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: $(MANPAGES)
+
+clean:
+ 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
Property changes on: trunk/packages/mipe/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/mipe/trunk/debian/watch
===================================================================
--- trunk/packages/mipe/trunk/debian/watch (rev 0)
+++ trunk/packages/mipe/trunk/debian/watch 2008-04-07 08:45:20 UTC (rev 1692)
@@ -0,0 +1,22 @@
+# Example watch control file for uscan
+# Rename this file to "watch" and then you can run the "uscan" command
+# to check for upstream updates and more.
+# See uscan(1) for format
+
+# Compulsory line, this is a version 3 file
+version=3
+
+# Uncomment to examine a Webpage
+# <Webpage URL> <string match>
+#http://www.example.com/downloads.php mipe-(.*)\.tar\.gz
+
+# Uncomment to examine a Webserver directory
+#http://www.example.com/pub/mipe-(.*)\.tar\.gz
+
+# Uncommment to examine a FTP server
+#ftp://ftp.example.com/pub/mipe-(.*)\.tar\.gz debian uupdate
+
+# Uncomment to use Roland's hack for sourceforge based projects - YMMV!
+http://people.debian.org/~lolando/sfdlr.php?project=mipe mipe-([\d.]*).tar.gz
+
+
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