[med-svn] [blasr] 07/12: Use externally packaged pbseqlib and dynamically link to it
Afif Elghraoui
afif-guest at moszumanska.debian.org
Mon Dec 14 21:14:43 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository blasr.
commit 18e9b0d9706a1e4dd6d0604cc89431b69024ce8d
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Sun Dec 13 13:03:19 2015 -0800
Use externally packaged pbseqlib and dynamically link to it
---
debian/control | 10 ++++--
debian/copyright | 61 ---------------------------------
debian/get-orig-source | 39 ---------------------
debian/patches/selective-static-linking | 31 -----------------
debian/patches/series | 1 -
debian/rules | 20 +++++------
6 files changed, 16 insertions(+), 146 deletions(-)
diff --git a/debian/control b/debian/control
index 297701c..ca35bbd 100644
--- a/debian/control
+++ b/debian/control
@@ -6,7 +6,10 @@ Uploaders: Afif Elghraoui <afif at ghraoui.name>
Build-Depends: debhelper (>= 9),
python,
libhdf5-dev,
- zlib1g-dev
+ zlib1g-dev,
+ libblasr-dev,
+ libpbdata-dev,
+ libpbihdf-dev,
Standards-Version: 3.9.6
Homepage: https://github.com/PacificBiosciences/blasr
Vcs-Git: git://anonscm.debian.org/debian-med/blasr.git
@@ -15,7 +18,10 @@ Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/blasr.git
Package: blasr
Architecture: any
Depends: ${shlibs:Depends},
- ${misc:Depends}
+ ${misc:Depends},
+ libblasr,
+ libpbdata,
+ libpbihdf,
Description: mapping single-molecule sequencing reads
Basic local alignment with successive refinement (BLASR) is a method
for mapping single-molecule sequencing reads against a reference genome.
diff --git a/debian/copyright b/debian/copyright
index 84a6bc3..60bbc6b 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -7,21 +7,6 @@ Files: *
Copyright: 2011-2015 Pacific Biosciences of California, Inc.
License: PacBio-BSD-3-Clause
-Files: libcpp/pbdata/MD5Utils.cpp
- libcpp/pbdata/MD5Utils.hpp
-Copyright: 1991-1992 RSA Data Security, Inc.
- 1995 Mordechai T. Abzug
-License: RSA
-
-Files: libcpp/alignment/algorithms/sorting/qsufsort.cpp
- libcpp/alignment/algorithms/sorting/qsufsort.hpp
-Copyright: 1999 N. Jesper Larsson <jesper at cs.lth.se>
-License: Larsson
-
-Files: libcpp/alignment/suffixarray/ssort.hpp
-Copyright: 1997 Lucent Technologies
-License: Lucent
-
Files: debian/*
Copyright: 2015 Afif Elghraoui <afif at ghraoui.name>
License: PacBio-BSD-3-Clause
@@ -52,49 +37,3 @@ License: PacBio-BSD-3-Clause
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN
IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-License: RSA
- License to copy and use this software is granted provided that it
- is identified as the "RSA Data Security, Inc. MD5 Message-Digest
- Algorithm" in all material mentioning or referencing this software
- or this function.
- .
- License is also granted to make and use derivative works provided
- that such works are identified as "derived from the RSA Data
- Security, Inc. MD5 Message-Digest Algorithm" in all material
- mentioning or referencing the derived work.
- .
- RSA Data Security, Inc. makes no representations concerning either
- the merchantability of this software or the suitability of this
- software for any particular purpose. It is provided "as is"
- without express or implied warranty of any kind.
- .
- These notices must be retained in any copies of any part of this
- documentation and/or software.
-
-License: Lucent
- Permission to use, copy, modify, and distribute this software and
- its documentation for any purpose and without fee is hereby
- granted, provided that the above copyright notice appear in all
- copies and that both that the copyright notice and this
- permission notice and warranty disclaimer appear in supporting
- documentation, and that the name Lucent Technologies or any of
- its entities not be used in advertising or publicity pertaining
- to distribution of the software without specific, written prior
- permission.
- .
- LUCENT DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,
- INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS.
- IN NO EVENT SHALL LUCENT OR ANY OF ITS ENTITIES BE LIABLE FOR ANY
- SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
- WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER
- IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION,
- ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF
- THIS SOFTWARE.
-
-License: Larsson
- This software may be used freely for any purpose. However, when distributed,
- the original source must be clearly stated, and, when the source code is
- distributed, the copyright notice must be retained and any alterations in
- the code must be clearly marked. No warranty is given regarding the quality
- of this software.
diff --git a/debian/get-orig-source b/debian/get-orig-source
deleted file mode 100755
index e19a66e..0000000
--- a/debian/get-orig-source
+++ /dev/null
@@ -1,39 +0,0 @@
-#!/bin/sh
-# if you need to repack for whatever reason you can
-# use this script via uscan or directly
-#
-# FIXME: currently the code is not conform to Debian Policy
-# http://www.debian.org/doc/debian-policy/ch-source.html
-# "get-orig-source (optional)"
-# This target may be invoked in any directory, ...
-# --> currently it is assumed the script is called in the
-# source directory featuring the debian/ dir
-
-COMPRESS=xz
-
-set -e
-NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
-
-if ! echo $@ | grep -q upstream-version ; then
- VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'`
- git clone --depth 1 --recursive \
- https://github.com/PacificBiosciences/blasr.git \
- ../${NAME}-${VERSION}
-else
- VERSION=`echo $@ | sed "s?^.*--upstream-version \([0-9.]\+\) .*${NAME}.*?\1?"`
- if echo "$VERSION" | grep -q "upstream-version" ; then
- echo "Unable to parse version number"
- exit
- fi
-fi
-
-TARDIR=${NAME}-${VERSION}
-mkdir -p ../tarballs
-cd ../tarballs
-
-# Remove useless files
-rm -rf ../${TARDIR}/.git*
-rm -rf ../${TARDIR}/libcpp/.git*
-
-GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.${COMPRESS} "../${TARDIR}"
-rm -rf ../${TARDIR}
diff --git a/debian/patches/selective-static-linking b/debian/patches/selective-static-linking
deleted file mode 100644
index 2f46cd0..0000000
--- a/debian/patches/selective-static-linking
+++ /dev/null
@@ -1,31 +0,0 @@
-Description: Static link only the internal libraries
- Libraries that are part of the source distribution are apparently only
- used by the binaries in this package, so they are probably best statically
- linked. Unfortunately, specifying static linking in the build system
- will statically link even zlib and other external libraries.
-Author: Afif Elghraoui <afif at ghraoui.name>
-Forwarded: no
-Last-Update: 2015-07-28
---- blasr.orig/configure.py
-+++ blasr/configure.py
-@@ -142,13 +142,13 @@
- 'LIBBLASR_LIB': os.path.join(ROOT, 'libcpp', 'alignment'),
- 'LIBPBDATA_LIB': os.path.join(ROOT, 'libcpp', 'pbdata'),
- 'LIBPBIHDF_LIB': os.path.join(ROOT, 'libcpp', 'hdf'),
-- 'LIBBLASR_LIBFLAGS': '-lblasr',
-- 'LIBPBDATA_LIBFLAGS': '-lpbdata',
-- 'LIBPBIHDF_LIBFLAGS': '-lpbihdf',
-- 'HDF5_LIBFLAGS': '-lhdf5_cpp -lhdf5',
-- 'ZLIB_LIBFLAGS': '-lz',
-- 'PTHREAD_LIBFLAGS': '-lpthread',
-- 'DL_LIBFLAGS': '-ldl', # neeeded by HDF5 always
-+ 'LIBBLASR_LIBFLAGS': '-Wl,-Bstatic -lblasr',
-+ 'LIBPBDATA_LIBFLAGS': '-Wl,-Bstatic -lpbdata',
-+ 'LIBPBIHDF_LIBFLAGS': '-Wl,-Bstatic -lpbihdf',
-+ 'HDF5_LIBFLAGS': '-Wl,-Bdynamic -lhdf5_cpp -lhdf5',
-+ 'ZLIB_LIBFLAGS': '-Wl,-Bdynamic -lz',
-+ 'PTHREAD_LIBFLAGS': '-Wl,-Bdynamic -lpthread',
-+ 'DL_LIBFLAGS': '-Wl,-Bdynamic -ldl', # neeeded by HDF5 always
- 'SHELL': 'bash -xe',
- }
- #setifenvf(defaults, env, 'OS_STRING', get_OS_STRING)
diff --git a/debian/patches/series b/debian/patches/series
index 4e9ea6e..e69de29 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +0,0 @@
-selective-static-linking
diff --git a/debian/rules b/debian/rules
index 527d645..cc6e61b 100755
--- a/debian/rules
+++ b/debian/rules
@@ -6,27 +6,23 @@ include /usr/share/dpkg/default.mk
export HDF5_INC=/usr/include/hdf5/serial
export HDF5_LIB=/usr/lib/$(DEB_HOST_MULTIARCH)/hdf5/serial
-# This is needed for libcpp/configure.py. The top-level configure.py
-# uses a command-line argument.
-export NOPBBAM=1
+export LIBBLASR_INC=/usr/include/blasr
+export LIBBLASR_LIB=/usr/lib/$(DEB_HOST_MULTIARCH)
+export LIBPBDATA_INC=/usr/include/pbdata
+export LIBPBDATA_LIB=/usr/lib/$(DEB_HOST_MULTIARCH)
+export LIBPBIHDF_INC=/usr/include/pbihdf
+export LIBPBIHDF_LIB=/usr/lib/$(DEB_HOST_MULTIARCH)
%:
dh $@
override_dh_auto_configure:
- ./configure.py --no-pbbam --submodules
- libcpp/configure.py
-
-override_dh_auto_build:
- $(MAKE) build-submodule
- $(MAKE)
+ ./configure.py --no-pbbam --shared
# Tests require cram. I don't find it available in Debian
override_dh_auto_test:
override_dh_auto_clean: override_dh_auto_configure
- $(MAKE) cleanall
+ $(MAKE) clean
# This is created by configure.py
rm -f defines.mk
- # These are created by libcpp/configure.py
- rm -f libcpp/defines.mk libcpp/pbdata/libconfig.h
--
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