[med-svn] r5874 - in trunk/packages/mosaik-aligner/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Thu Feb 3 15:35:34 UTC 2011
Author: tille
Date: 2011-02-03 15:35:29 +0000 (Thu, 03 Feb 2011)
New Revision: 5874
Added:
trunk/packages/mosaik-aligner/trunk/debian/README.source
trunk/packages/mosaik-aligner/trunk/debian/copyright
trunk/packages/mosaik-aligner/trunk/debian/dirs
trunk/packages/mosaik-aligner/trunk/debian/get-orig-source
trunk/packages/mosaik-aligner/trunk/debian/patches/
trunk/packages/mosaik-aligner/trunk/debian/patches/no_static_linking.patch
trunk/packages/mosaik-aligner/trunk/debian/patches/series
trunk/packages/mosaik-aligner/trunk/debian/patches/use_debian_packaged_sqlite.patch
Modified:
trunk/packages/mosaik-aligner/trunk/debian/changelog
trunk/packages/mosaik-aligner/trunk/debian/control
trunk/packages/mosaik-aligner/trunk/debian/rules
Log:
Proper copyright file, create manpages via help2man, dynamic instead of static linking, remove copy of sqlite from source and rather use Debian packaged version
Added: trunk/packages/mosaik-aligner/trunk/debian/README.source
===================================================================
--- trunk/packages/mosaik-aligner/trunk/debian/README.source (rev 0)
+++ trunk/packages/mosaik-aligner/trunk/debian/README.source 2011-02-03 15:35:29 UTC (rev 5874)
@@ -0,0 +1,6 @@
+When building the source tarball the internal copy of sqlite was stripped
+to rather use the Debian packaged version of this library. The relevant
+Makefiles are patched in this process to get an easily buildable upstream
+source also for other purposes.
+
+ -- Andreas Tille <tille at debian.org> Thu, 03 Feb 2011 14:10:47 +0100
Modified: trunk/packages/mosaik-aligner/trunk/debian/changelog
===================================================================
--- trunk/packages/mosaik-aligner/trunk/debian/changelog 2011-02-03 15:31:09 UTC (rev 5873)
+++ trunk/packages/mosaik-aligner/trunk/debian/changelog 2011-02-03 15:35:29 UTC (rev 5874)
@@ -2,4 +2,4 @@
* Initial release (Closes: #????)
- -- Andreas Tille <tille at debian.org> Sun, 30 Jan 2011 18:41:07 +0100
+ -- Andreas Tille <tille at debian.org> Thu, 03 Feb 2011 14:10:47 +0100
Modified: trunk/packages/mosaik-aligner/trunk/debian/control
===================================================================
--- trunk/packages/mosaik-aligner/trunk/debian/control 2011-02-03 15:31:09 UTC (rev 5873)
+++ trunk/packages/mosaik-aligner/trunk/debian/control 2011-02-03 15:35:29 UTC (rev 5874)
@@ -4,7 +4,7 @@
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 7.1), zlib1g-dev, help2man
+Build-Depends: debhelper (>= 7.1), quilt (>=0.47), zlib1g-dev, libsqlite3-dev, help2man
Standards-Version: 3.9.1
Homepage: http://code.google.com/p/mosaik-aligner/
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mosaik-aligner/trunk
Added: trunk/packages/mosaik-aligner/trunk/debian/copyright
===================================================================
--- trunk/packages/mosaik-aligner/trunk/debian/copyright (rev 0)
+++ trunk/packages/mosaik-aligner/trunk/debian/copyright 2011-02-03 15:35:29 UTC (rev 5874)
@@ -0,0 +1,37 @@
+Format: http://dep.debian.net/deps/dep5/
+Upstream-Name: Mosaik
+Upstream-Contact: Wan-Ping <wanping.lee at gmail.com>
+Source: http://code.google.com/p/mosaik-aligner/
+
+Files: *
+Copyright: © 2009-2010 Michael Stromberg & Wan-Ping Lee
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
+
+Files: src/CommonSource/Utilities/sqlite3.*
+Upstream Author: D. Richard Hipp <drh at hwaci.com>
+Copyright: The author disclaims all copyright.
+License: Public Domain
+Remark: This code was stripped from original tarball and the Debian packaged
+ sqlite is used
+
+Files: debian/*
+Copyright: © 2011 Andreas Tille <tille at debian.org>
+License: PD
+ The packaging work is in the public domain unless stated otherwise.
Added: trunk/packages/mosaik-aligner/trunk/debian/dirs
===================================================================
--- trunk/packages/mosaik-aligner/trunk/debian/dirs (rev 0)
+++ trunk/packages/mosaik-aligner/trunk/debian/dirs 2011-02-03 15:35:29 UTC (rev 5874)
@@ -0,0 +1 @@
+usr/share/man/man1
Added: trunk/packages/mosaik-aligner/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/mosaik-aligner/trunk/debian/get-orig-source (rev 0)
+++ trunk/packages/mosaik-aligner/trunk/debian/get-orig-source 2011-02-03 15:35:29 UTC (rev 5874)
@@ -0,0 +1,32 @@
+#!/bin/sh -e
+# script to download and repack source package of mosaik-aligner to get rid of sqlite copy
+
+PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+VERSION=`uscan --verbose --force-download | \
+ grep "Newest version on remote site is .* local version is .*" | \
+ head -n 1 | \
+ sed "s/Newest version on remote site is \([-0-9.]\+\),.*/\1/"`
+
+CURDIR=`pwd`
+
+mkdir -p ../tarballs
+cd ../tarballs
+
+set -x
+
+UPSTREAMDIR=${PKG}
+tar -xjf ../Mosaik-${VERSION}-source.tar.bz2
+cd ${PKG}
+
+# remove copy of sqlite
+rm -f src/CommonSource/Utilities/sqlite3.[ch]
+patch -p1 < ${CURDIR}/debian/patches/use_debian_packaged_sqlite.patch
+
+# clean up other unneeded cruft from source tarball once we are repackaging it
+find . -name ".*.swp" -exec rm -f \{\} \;
+rm -rf src/VisualStudio
+cd ..
+
+BZIP2="--best" tar -cjf "$PKG"_"$VERSION".orig.tar.bz2 "${UPSTREAMDIR}"
+rm -rf "${UPSTREAMDIR}"
+
Added: trunk/packages/mosaik-aligner/trunk/debian/patches/no_static_linking.patch
===================================================================
--- trunk/packages/mosaik-aligner/trunk/debian/patches/no_static_linking.patch (rev 0)
+++ trunk/packages/mosaik-aligner/trunk/debian/patches/no_static_linking.patch 2011-02-03 15:35:29 UTC (rev 5874)
@@ -0,0 +1,10 @@
+Author: Andreas Tille <tille at debian.org>
+Date: Thu, 03 Feb 2011 14:10:47 +0100
+Description: Do not force static linking
+
+--- mosaik-aligner.orig/src/includes/linux.inc
++++ mosaik-aligner/src/includes/linux.inc
+@@ -1,2 +1,2 @@
+ # define our processor specific flags
+-export PLATFORM_FLAGS = -D_FILE_OFFSET_BITS=64 -static
++export PLATFORM_FLAGS = -D_FILE_OFFSET_BITS=64
Added: trunk/packages/mosaik-aligner/trunk/debian/patches/series
===================================================================
--- trunk/packages/mosaik-aligner/trunk/debian/patches/series (rev 0)
+++ trunk/packages/mosaik-aligner/trunk/debian/patches/series 2011-02-03 15:35:29 UTC (rev 5874)
@@ -0,0 +1 @@
+no_static_linking.patch
Added: trunk/packages/mosaik-aligner/trunk/debian/patches/use_debian_packaged_sqlite.patch
===================================================================
--- trunk/packages/mosaik-aligner/trunk/debian/patches/use_debian_packaged_sqlite.patch (rev 0)
+++ trunk/packages/mosaik-aligner/trunk/debian/patches/use_debian_packaged_sqlite.patch 2011-02-03 15:35:29 UTC (rev 5874)
@@ -0,0 +1,33 @@
+Note: This patch is applied in the debian/get-orig-source target to enable
+ other users of this script a working build system
+Author: Andreas Tille
+Date: Thu, 03 Feb 2011 14:10:47 +0100
+Description: Do not use sqlite shipped with this source
+
+--- mosaik-aligner.orig/src/CommonSource/Utilities/Makefile
++++ mosaik-aligner/src/CommonSource/Utilities/Makefile
+@@ -16,7 +16,7 @@
+ OBJECTS= $(SOURCES:.cpp=.o)
+ BUILT_OBJECTS= $(patsubst %,$(TD)$(OBJ_DIR)/%,$(OBJECTS))
+
+-CSOURCES = fastlz.c MD5.c sqlite3.c
++CSOURCES = fastlz.c MD5.c
+ COBJECTS= $(CSOURCES:.c=.o)
+ CBUILT_OBJECTS= $(patsubst %,$(TD)$(OBJ_DIR)/%,$(COBJECTS))
+
+--- mosaik-aligner.orig/src/MosaikSort/Makefile
++++ mosaik-aligner/src/MosaikSort/Makefile
+@@ -14,11 +14,11 @@
+ # ----------------------------------
+ SOURCES= PairedEndSort.cpp SortMain.cpp SingleEndSort.cpp
+ OBJECTS= $(SOURCES:.cpp=.o)
+-_EXT_OBJECTS= AlignmentQuality.o AlignmentReader.o AlignmentWriter.o Benchmark.o ConsoleUtilities.o fastlz.o FastLZIO.o FileUtilities.o MemoryUtilities.o MosaikString.o NaiveAlignmentSet.o Options.o SequenceUtilities.o SHA1.o sqlite3.o TimeSupport.o
++_EXT_OBJECTS= AlignmentQuality.o AlignmentReader.o AlignmentWriter.o Benchmark.o ConsoleUtilities.o fastlz.o FastLZIO.o FileUtilities.o MemoryUtilities.o MosaikString.o NaiveAlignmentSet.o Options.o SequenceUtilities.o SHA1.o TimeSupport.o
+ EXT_OBJECTS=$(patsubst %,$(TD)$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+ BUILT_OBJECTS= $(patsubst %,$(TD)$(OBJ_DIR)/%,$(OBJECTS))
+ PROGRAM= MosaikSort
+-LIBS= $(PLATFORM_LIBS) -lpthread
++LIBS= $(PLATFORM_LIBS) -lpthread -lsqlite3
+
+ all: $(PROGRAM)
+
Modified: trunk/packages/mosaik-aligner/trunk/debian/rules
===================================================================
--- trunk/packages/mosaik-aligner/trunk/debian/rules 2011-02-03 15:31:09 UTC (rev 5873)
+++ trunk/packages/mosaik-aligner/trunk/debian/rules 2011-02-03 15:35:29 UTC (rev 5874)
@@ -9,14 +9,32 @@
pkg=mosaik-aligner
%:
- dh $@
+ dh $@ --with quilt
override_dh_auto_build:
cd src; $(MAKE)
- mkdir -p $(CURDIR)/debian/$(pkg)/usr/share/man/man1/
- for bin in MosaikAligner MosaikMerge MosaikSort ; do \
- help2man --no-info $(CURDIR)/bin/$${bin} > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/$${bin}.1 ; \
- done
+override_dh_auto_install:
+ help2man --no-info --name="pairwise alignment of MOSAIK read files" $(CURDIR)/bin/MosaikAligner \
+ > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/MosaikAligner.1
+ help2man --no-info --name="produce an assembly file from a MOSAIK alignment file" $(CURDIR)/bin/MosaikAssembler \
+ > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/MosaikAssembler.1
+ help2man --no-info --name="convert external read formats to native MOSAIK formats" $(CURDIR)/bin/MosaikBuild \
+ > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/MosaikBuild.1
+ help2man --no-info --name="merge several sorted MOSAIK alignment files" $(CURDIR)/bin/MosaikMerge \
+ > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/MosaikMerge.1
+ help2man --no-info --name="sort the alignments by position" $(CURDIR)/bin/MosaikSort \
+ > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/MosaikSort.1
+
+ echo "Running the test suite"
+ cd data ; \
+ ./Build.sh ; \
+ ./Align.sh ; \
+ ./Assemble.sh
+
+
override_dh_auto_clean:
cd src; $(MAKE) clean
+
+get-orig-source:
+ . debian/get-orig-source
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