[med-svn] [libgkarrays] 02/02: Inject as somewhat hackish packaging which avoids an extra libprogressbar package
Andreas Tille
tille at debian.org
Mon Sep 12 11:02:19 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository libgkarrays.
commit ac7a0a72f6fd184a01739ab2a1916428b4fc51f3
Author: Andreas Tille <tille at debian.org>
Date: Mon Sep 12 13:01:00 2016 +0200
Inject as somewhat hackish packaging which avoids an extra libprogressbar package
---
debian/changelog | 5 +
debian/compat | 1 +
debian/control | 51 ++++
debian/copyright | 536 +++++++++++++++++++++++++++++++++++++
debian/patches/proper_soname.patch | 27 ++
debian/patches/series | 1 +
debian/rules | 33 +++
debian/source/format | 1 +
debian/upstream/metadata | 10 +
debian/watch | 3 +
10 files changed, 668 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..468c308
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+libgkarrays (2.1.0-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Sat, 10 Sep 2016 23:41:37 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..f83e09a
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,51 @@
+Source: libgkarrays
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Anthony Boureux <Anthony.Boureux at gmail.com>,
+ Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ dh-autoreconf,
+ d-shlibs,
+ zlib1g-dev
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libgkarrays.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/libgkarrays.git
+Homepage: http://crac.gforge.inria.fr/gkarrays/
+
+Package: libgkarrays1
+Architecture: any
+Section: libs
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: library to query large collection of NGS sequences
+ Gk-arrays are provided as a simple-to-use C++ library dedicated to
+ queries on large collection of sequences as produced by high-throughput
+ sequencers (e.g. HiSeq 2000 from Illumina, 454 from Roche).
+ .
+ Gk-arrays index k-mers of reads and allow to answer different queries on
+ that read collection (e.g. how many reads share this k-mer? where does
+ this k-mer occur in the read collection?).
+ .
+ Gk-arrays consist of a space-efficient alternative to hash tables while
+ being similar in terms of query times.
+
+Package: libgkarrays-dev
+Architecture: any
+Section: libdevel
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ libgkarrays1 (= ${binary:Version})
+Description: library to query large collection of NGS sequences (development)
+ Gk-arrays are provided as a simple-to-use C++ library dedicated to
+ queries on large collection of sequences as produced by high-throughput
+ sequencers (e.g. HiSeq 2000 from Illumina, 454 from Roche).
+ .
+ Gk-arrays index k-mers of reads and allow to answer different queries on
+ that read collection (e.g. how many reads share this k-mer? where does
+ this k-mer occur in the read collection?).
+ .
+ Gk-arrays consist of a space-efficient alternative to hash tables while
+ being similar in terms of query times.
+ .
+ This is the development library for libgkarrays.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..8022221
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,536 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Gk-arrays
+Source: http://crac.gforge.inria.fr
+
+Files: *
+Copyright: © 2012-2014 by Nicolas PHILIPPE <nicolas.philippe at lirmm.fr>
+ © 2012-2014 by Mikaël SALSON <mikael.salson at lifl.fr>
+ © 2012-2014 by Alban MANCHERON <alban.mancheron at lirmm.fr>
+ © 2013-2014 by Jérôme Audoux <Jerome.Audoux at gmail.com>
+License: CeCILL
+
+Files: debian/*
+Copyright: 2014 Anthony Boureux <Anthony.Boureux at gmail.com>
+License: GPL-2+
+ This package 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.
+ .
+ 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 General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+License: CeCILL
+ CeCILL FREE SOFTWARE LICENSE AGREEMENT
+ .
+ Notice
+ .
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+ intellectual property law, and the protection that it offers to
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+ .
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diff --git a/debian/patches/proper_soname.patch b/debian/patches/proper_soname.patch
new file mode 100644
index 0000000..62a2c57
--- /dev/null
+++ b/debian/patches/proper_soname.patch
@@ -0,0 +1,27 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sat, 10 Sep 2016 23:41:37 +0200
+Description: Droping -release from LDFLAGS since otherwise a broken soname
+ is created
+
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -138,7 +138,7 @@ libGkArrays_ladir = @abs_srcdir@
+ libGkArrays_la_SOURCES = gkArrays.cpp solArray.cpp utils.cpp gkArraysBuilder.cpp gkSABuilder.cpp gkCFPSBuilder.cpp gkIFABuilder.cpp readsReader.cpp largebinvect.cxx bitvector.cxx $(SUX_SRCS)
+ libGkArrays_la_configdir = @libdir@/@PACKAGE at -@VERSION@/include
+ libGkArrays_la_config_DATA = @abs_top_builddir@/config/config.h
+-libGkArrays_la_LDFLAGS = -version-info @LIB_VERSION@ -release @VERSION@ $(AM_LDFLAGS) # @LIBDIVSUFSORT@
++libGkArrays_la_LDFLAGS = -version-info @LIB_VERSION@ $(AM_LDFLAGS) # @LIBDIVSUFSORT@
+
+ if INCLUDED_PROGRESSBAR
+ AM_LDFLAGS += -L at abs_builddir@/libProgressBar-1.2.0/libProgressBar/.libs -lProgressBar
+--- a/src/libProgressBar-1.2.0/libProgressBar/Makefile.am
++++ b/src/libProgressBar-1.2.0/libProgressBar/Makefile.am
+@@ -4,7 +4,7 @@ lib_LTLIBRARIES = libProgressBar.la
+ libProgressBar_la_SOURCES = progressBar.h progressBar.cpp
+ libProgressBar_la_configdir = @libdir@/@PACKAGE at -@VERSION@/include
+ libProgressBar_la_config_DATA = config.h
+-libProgressBar_la_LDFLAGS = -version-info @LIB_VERSION@ -release @VERSION@ $(AM_LDFLAGS)
++libProgressBar_la_LDFLAGS = -version-info @LIB_VERSION@ $(AM_LDFLAGS)
+
+ noinst_PROGRAMS=testProgressBar
+ testProgressBar_SOURCES=testPB.cpp
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..e592159
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+proper_soname.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..deec47c
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,33 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+VERSION := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+
+%:
+ dh $@ --with autoreconf
+
+override_dh_install:
+ dh_install
+ rm -f debian/tmp/usr/include/libGkArrays-*/*.cxx
+ # find debian/tmp/usr/include -type l -delete
+ d-shlibmove --commit \
+ --multiarch \
+ --devunversioned \
+ --exclude-la \
+ --override s/libProgressBar0-dev/zlib1g-dev/ \
+ --movedev debian/tmp/usr/include/libGkArrays-$(VERSION)/ usr/include \
+ --movedev debian/tmp/usr/include/libProgressBar-1.2.0/ usr/include \
+ --movedev debian/tmp/usr/lib/$(DEB_HOST_MULTIARCH)/pkgconfig usr/lib/$(DEB_HOST_MULTIARCH) \
+ debian/tmp/usr/lib/$(DEB_HOST_MULTIARCH)/libGkArrays.so
+ # now move libProgressBar manually
+ mv debian/tmp/usr/lib/$(DEB_HOST_MULTIARCH)/libProgressBar.so.0* debian/libgkarrays1/usr/lib/$(DEB_HOST_MULTIARCH)
+ chmod -x debian/libgkarrays1/usr/lib/$(DEB_HOST_MULTIARCH)/libProgressBar.so.0.*
+ mv debian/tmp/usr/lib/$(DEB_HOST_MULTIARCH)/libProgressBar.so debian/libgkarrays-dev/usr/lib/$(DEB_HOST_MULTIARCH)
+ mv debian/tmp/usr/lib/$(DEB_HOST_MULTIARCH)/libProgressBar.a debian/libgkarrays-dev/usr/lib/$(DEB_HOST_MULTIARCH)
+
+# the override is pure cheating since otherwise we's need to package zlib1g-dev separately
+#
+# d-shlibmove --commit --multiarch --devunversioned --override s/libProgressBar0-dev/libbpp-seq-dev/ debian/tmp/usr/lib/*/libGkArrays.so
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..6b7a678
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,10 @@
+Reference:
+ Author: Nicolas Philippe and Mikaël Salson and Thierry Lecroq and Martine Léonard and Thérèse Commes and Eric Rivals
+ Title: "Querying large read collections in main memory: a versatile data structure"
+ Journal: BMC Bioinformatics
+ Volume: 12
+ Pages: 242
+ Year: 2011
+ DOI: 10.1186/1471-2105-12-242
+ PMID: 21682852
+ URL: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-242
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..88f4260
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+
+http://gforge.inria.fr/frs/?group_id=3008 .*/libGkArrays-(.*)\.tar\.gz
--
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