[med-svn] [Git][med-team/pbdagcon][master] 8 commits: checkout submodules for code copy of DALIGNER and DAZZ_DB which are specific…
Andreas Tille
gitlab at salsa.debian.org
Thu Aug 16 15:12:58 BST 2018
Andreas Tille pushed to branch master at Debian Med / pbdagcon
Commits:
410f60ac by Andreas Tille at 2018-08-16T13:42:53Z
checkout submodules for code copy of DALIGNER and DAZZ_DB which are specific adaptations to pbdagcon
- - - - -
81358cad by Andreas Tille at 2018-08-16T13:44:43Z
New upstream version 0.3+git20180411.c14c422+ds
- - - - -
62b820cc by Andreas Tille at 2018-08-16T13:44:43Z
Update upstream source from tag 'upstream/0.3+git20180411.c14c422+ds'
Update to upstream version '0.3+git20180411.c14c422+ds'
with Debian dir a85d18131f664b4e13635b99b42c9c537411ca52
- - - - -
188a976b by Andreas Tille at 2018-08-16T13:48:13Z
Adapt patches
- - - - -
b4d560f6 by Andreas Tille at 2018-08-16T13:49:06Z
debhelper 11
- - - - -
453a82f2 by Andreas Tille at 2018-08-16T13:52:50Z
Point Vcs fields to salsa.debian.org
- - - - -
a1051d52 by Andreas Tille at 2018-08-16T13:52:50Z
Standards-Version: 4.2.0
- - - - -
7444cf1a by Andreas Tille at 2018-08-16T14:08:55Z
Add new include
- - - - -
18 changed files:
- README.md
- + bamboo_build.sh
- + bamboo_test.sh
- configure.py
- debian/changelog
- debian/compat
- debian/control
- debian/get-orig-source
- debian/patches/compiler-flags.patch
- debian/rules
- debian/watch
- src/cpp/DazAlnProvider.cpp
- src/cpp/DazAlnProvider.hpp
- src/cpp/makefile
- src/filterm4.py
- src/m4topre.py
- src/q-sense.py
- test/cpp/makefile
Changes:
=====================================
README.md
=====================================
--- a/README.md
+++ b/README.md
@@ -130,3 +130,7 @@ ga('send', 'pageview');
src/filterm4.py 'code'
[pbdagcon_wf.sh]:
src/cpp/pbdagcon_wf.sh 'code'
+
+DISCLAIMER
+----------
+THIS WEBSITE AND CONTENT AND ALL SITE-RELATED SERVICES, INCLUDING ANY DATA, ARE PROVIDED "AS IS," WITH ALL FAULTS, WITH NO REPRESENTATIONS OR WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT OR FITNESS FOR A PARTICULAR PURPOSE. YOU ASSUME TOTAL RESPONSIBILITY AND RISK FOR YOUR USE OF THIS SITE, ALL SITE-RELATED SERVICES, AND ANY THIRD PARTY WEBSITES OR APPLICATIONS. NO ORAL OR WRITTEN INFORMATION OR ADVICE SHALL CREATE A WARRANTY OF ANY KIND. ANY REFERENCES TO SPECIFIC PRODUCTS OR SERVICES ON THE WEBSITES DO NOT CONSTITUTE OR IMPLY A RECOMMENDATION OR ENDORSEMENT BY PACIFIC BIOSCIENCES.
=====================================
bamboo_build.sh
=====================================
--- /dev/null
+++ b/bamboo_build.sh
@@ -0,0 +1,75 @@
+#!/bin/bash
+set -e
+NEXUS_BASEURL=http://ossnexus.pacificbiosciences.com/repository
+#NEXUS_URL=$NEXUS_BASEURL/unsupported/gcc-4.9.2
+if [ ! -e .distfiles/gtest/release-1.7.0.tar.gz ]; then
+ mkdir -p .distfiles/gtest
+ curl -sL $NEXUS_BASEURL/unsupported/distfiles/googletest/release-1.7.0.tar.gz \
+ -o .distfiles/gtest/release-1.7.0.tar.gz
+fi
+tar zxf .distfiles/gtest/release-1.7.0.tar.gz -C repos/
+ln -sfn googletest-release-1.7.0 repos/gtest
+
+rm -rf deployment
+mkdir -p deployment
+/bin/ls -t tarballs/pbbam-*.tgz | head -1 | xargs -r -n 1 cat | tar zxv --strip-components 3 -C deployment
+/bin/ls -t tarballs/blasr_libcpp-*.tgz | head -1 | xargs -r -n 1 cat | tar zxv --strip-components 3 -C deployment
+/bin/ls -t tarballs/blasr-*.tgz | head -1 | xargs -r -n 1 cat | tar zxv --strip-components 2 -C deployment
+DEPLOYMENT=$PWD/deployment
+
+export PATH=$PWD/deployment/bin:$PATH
+export LD_LIBRARY_PATH=$PWD/deployment/lib:$LD_LIBRARY_PATH
+
+type module >& /dev/null || . /mnt/software/Modules/current/init/bash
+module load git
+module load gcc
+module load ccache
+if [[ $USER == bamboo ]]; then
+ export CCACHE_DIR=/mnt/secondary/Share/tmp/bamboo.mobs.ccachedir
+fi
+module load boost
+if [[ $BOOST_ROOT =~ /include ]]; then
+ set -x
+ BOOST_ROOT=$(dirname $BOOST_ROOT)
+ set +x
+fi
+module load htslib
+module load hdf5-tools
+module load zlib
+
+DAZZDB=$PWD/repos/dazzdb
+DALIGNER=$PWD/repos/daligner
+cd repos/pbdagcon
+export CCACHE_BASEDIR=$PWD
+rm -rf build
+set -x
+mkdir -p build
+ BOOST_INCLUDE=$BOOST_ROOT/include \
+LIBPBDATA_INCLUDE=$DEPLOYMENT/include/pbdata \
+ LIBPBDATA_LIB=$DEPLOYMENT/lib \
+ LIBBLASR_INCLUDE=$DEPLOYMENT/include/alignment \
+ LIBBLASR_LIB=$DEPLOYMENT/lib \
+LIBPBIHDF_INCLUDE=$DEPLOYMENT/include/hdf \
+ LIBPBIHDF_LIB=$DEPLOYMENT/lib \
+ PBBAM_INCLUDE=$DEPLOYMENT/include \
+ PBBAM_LIB=$DEPLOYMENT/lib \
+ HTSLIB_CFLAGS=$(pkg-config --cflags htslib) \
+ HTSLIB_LIBS=$(pkg-config --libs htslib) \
+ HDF5_INCLUDE=$(pkg-config --cflags-only-I hdf5|awk '{print $1}'|sed -e 's/^-I//') \
+ HDF5_LIB=$(pkg-config --libs-only-L hdf5|awk '{print $1}'|sed -e 's/^-L//') \
+ DALIGNER_SRC=$DALIGNER \
+ DAZZ_DB_SRC=$DAZZDB \
+ GTEST_SRC=$PWD/../gtest/src \
+ GTEST_INCLUDE=$PWD/../gtest/include \
+ ZLIB_LIBFLAGS="$(pkg-config --libs zlib)" \
+./configure.py --build-dir=$PWD/build
+sed -i -e 's/-lpbihdf/-llibcpp/;s/-lblasr//;s/-lpbdata//' build/defines.mk
+make -C build
+cp -a build/src/cpp/pbdagcon $DEPLOYMENT/bin/
+cp -a build/src/cpp/dazcon $DEPLOYMENT/bin/
+cd ../..
+
+myVERSION=`pbdagcon --version|awk '/version/{print $3}'`
+#rm -rf tarballs && mkdir -p tarballs
+cd deployment
+tar zcf ../tarballs/pbdagcon-${myVERSION}.tgz bin/pbdagcon bin/dazcon
=====================================
bamboo_test.sh
=====================================
--- /dev/null
+++ b/bamboo_test.sh
@@ -0,0 +1,12 @@
+#!/bin/bash
+export PATH=$PWD/deployment/bin:$PATH
+export LD_LIBRARY_PATH=$PWD/deployment/lib:$LD_LIBRARY_PATH
+type module >& /dev/null \
+|| . /mnt/software/Modules/current/init/bash
+module load gcc
+module load htslib
+module load hdf5-tools
+module load zlib
+
+make -C repos/pbdagcon/build check
+chmod +w -R repos/pbdagcon
=====================================
configure.py
=====================================
--- a/configure.py
+++ b/configure.py
@@ -152,8 +152,8 @@ def compose_defines_pacbio(envin):
'LIBPBIHDF_INCLUDE', 'LIBPBIHDF_LIB', 'LIBPBIHDF_LIBFLAGS',
'HDF5_INCLUDE', 'HDF5_LIB', 'HDF5_LIBFLAGS',
'PBBAM_INCLUDE', 'PBBAM_LIB', 'PBBAM_LIBFLAGS',
- 'HTSLIB_INCLUDE', 'HTSLIB_LIB', 'HTSLIB_LIBFLAGS',
- 'BOOST_INCLUDE','PTHREAD_LIBFLAGS',
+ 'HTSLIB_CFLAGS', 'HTSLIB_LIBS',
+ 'BOOST_INCLUDE', 'PTHREAD_LIBFLAGS',
'ZLIB_LIB', 'ZLIB_LIBFLAGS',
'GCC_LIB',
'DAZZ_DB_SRC', 'DAZZ_DB_INCLUDE',
@@ -244,7 +244,7 @@ def set_defs_defaults(env, nopbbam):
pbbam_defaults = {
'LIBPBIHDF_LIBFLAGS': '-lpbihdf',
'PBBAM_LIBFLAGS': '-lpbbam',
- 'HTSLIB_LIBFLAGS': '-lhts',
+ 'HTSLIB_LIBS': '-lhts',
'HDF5_LIBFLAGS': '-lhdf5_cpp -lhdf5',
'ZLIB_LIBFLAGS': '-lz',
'PTHREAD_LIBFLAGS': '-lpthread',
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -6,9 +6,12 @@ pbdagcon (0.3+git20180411.c14c422+ds-1) UNRELEASED; urgency=low
* Add README.source
[ Andreas Tille ]
- * d/watch: use git mode
- TODO: Clarify role of code copies pointing to outdated versions of
- daligner and dazzdb packages
+ * d/watch: use git mode to detect new upstream commit
+ * d/get-orig-source: checkout submodules for code copy of DALIGNER and
+ DAZZ_DB which are specific adaptations to pbdagcon
+ * debhelper 11
+ * Point Vcs fields to salsa.debian.org
+ * Standards-Version: 4.2.0
-- Andreas Tille <tille at debian.org> Thu, 19 Jul 2018 11:25:43 +0200
=====================================
debian/compat
=====================================
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-10
+11
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -1,34 +1,30 @@
Source: pbdagcon
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Afif Elghraoui <afif at debian.org>
Section: science
Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders:
- Afif Elghraoui <afif at debian.org>,
-Build-Depends:
- debhelper (>= 10),
- python,
- zlib1g-dev,
- libhdf5-dev,
- libboost-dev,
- libtclap-dev,
- libpbseq-dev,
- libpbbam-dev,
+Build-Depends: debhelper (>= 11~),
+ python,
+ zlib1g-dev,
+ libhdf5-dev,
+ libboost-dev,
+ libtclap-dev,
+ libpbseq-dev,
+ libpbbam-dev,
# Test-Depends:
- googletest,
-Standards-Version: 3.9.8
+ googletest
+Standards-Version: 4.2.0
+Vcs-Browser: https://salsa.debian.org/med-team/pbdagcon
+Vcs-Git: https://salsa.debian.org/med-team/pbdagcon.git
Homepage: https://github.com/PacificBiosciences/pbdagcon
-Vcs-Git: https://anonscm.debian.org/git/debian-med/pbdagcon.git
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/pbdagcon.git
Package: pbdagcon
Architecture: any
-Depends:
- ${shlibs:Depends},
- ${misc:Depends},
- libpbseq,
- libpbbam,
-Suggests:
- blasr,
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ libpbseq,
+ libpbbam
+Suggests: blasr
Description: sequence consensus using directed acyclic graphs
pbdagcon is a tool that implements DAGCon (Directed Acyclic Graph Consensus)
which is a sequence consensus algorithm based on using directed acyclic
=====================================
debian/get-orig-source
=====================================
--- a/debian/get-orig-source
+++ b/debian/get-orig-source
@@ -8,28 +8,50 @@ PKGDIR="$PWD"
# using source package name $SPKG from debian/changelog
# This makes it more robust for newer uupdate in future
SPKG=$(dpkg-parsechangelog -SSource)
-NEW_VERSION=$(dpkg-parsechangelog -SVersion | sed 's/\-[0-9]*$//')
+
+#NEW_VERSION=$(dpkg-parsechangelog -SVersion | sed 's/\-[0-9]*$//')
+
+if ! echo $@ | grep -q upstream-version ; then
+ NEW_VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed -e 's/+ds[0-9]*//' -e 's/\([0-9\.]\+\)-[0-9]\+$/\1/'`
+ uscan --force-download
+else
+ NEW_VERSION=`echo $@ | sed "s?^.*--upstream-version \([0-9.+gitabcdef]\+\)+ds.*?\1?"`
+ if echo "$VERSION" | grep -q "upstream-version" ; then
+ echo "Unable to parse version number"
+ exit
+ fi
+fi
+
new_package="${SPKG}-${NEW_VERSION}"
clean () {
- rm -rf ../${new_package} ../${SPKG}-${NEW_VERSION}.tar.gz
+ rm -rf ../${new_package} ../${SPKG}.tmp.tar.gz
}
trap clean EXIT
cd ..
-# Now ${SPKG}_${NEW_VERSION}.orig.tar.xz is upstream tarball
-rm -f ${SPKG}_${NEW_VERSION}.orig.tar.*
+# Remove original download since its lacking DALIGNER and DAZZ_DB
+rm -f ${SPKG}-${NEW_VERSION}.tar.[gx]z
+# since daligner und dazz_db are needed and are only provided
+# as submodules and this old code seems to be really needed
+# see https://lists.debian.org/debian-med/2018/07/msg00088.html
echo "Cloning ${SPKG} version ${NEW_VERSION}"
git clone \
https://github.com/PacificBiosciences/pbdagcon.git $new_package
-cd $new_package \
- && make update-submodule \
- && rm -rf blasr_libcpp \
- && find -name ".git*" -exec rm -rf {} + \
- && cd $PKGDIR
-
-tar -czf ../${SPKG}-${NEW_VERSION}.tar.gz ../${new_package}
-mk-origtargz --compression xz ../${SPKG}-${NEW_VERSION}.tar.gz
+cd $new_package
+# Add "|| true" since it returns:
+# Fetched in submodule path 'blasr_libcpp', but it did not contain 9b4faa3efa2d59484af3c3562a3af6ce421e0294. Direct fetching of that commit failed.
+# makefile:22: recipe for target 'update-submodule' failed
+make update-submodule || true
+# debug
+# ls -l DALIGNER
+# ls -l DAZZ_DB
+rm -rf blasr_libcpp
+find -name ".git*" | xargs rm -rf
+cd $PKGDIR
+
+tar -czf ../${SPKG}.tmp.tar.gz ../${new_package}
+mk-origtargz --compression xz --repack --version ${NEW_VERSION}+ds ../${SPKG}.tmp.tar.gz
=====================================
debian/patches/compiler-flags.patch
=====================================
--- a/debian/patches/compiler-flags.patch
+++ b/debian/patches/compiler-flags.patch
@@ -2,15 +2,15 @@ Description: Prevent override of dpkg-buildflags
Author: Afif Elghraoui <afif at debian.org>
Forwarded: no
Last-Update: 2016-10-23
---- pbdagcon.orig/src/cpp/makefile
-+++ pbdagcon/src/cpp/makefile
-@@ -8,8 +8,8 @@
+--- a/src/cpp/makefile
++++ b/src/cpp/makefile
+@@ -8,8 +8,8 @@ PBDAGCON_OBJECTS := BlasrM5AlnProvider.o
DAZCON_OBJECTS := DB.o QV.o align.o DazAlnProvider.o dazcon.o
CPPFLAGS += -MMD -MP
--CXXFLAGS = -O3 -std=c++11 -Wall -Wuninitialized -pedantic
+-CXXFLAGS = -O3 -std=c++14 -Wall -Wuninitialized -pedantic
-CFLAGS = -O3 -Wall -Wextra -fno-strict-aliasing
-+CXXFLAGS += -O3 -std=c++11 -Wall -Wuninitialized -pedantic
++CXXFLAGS += -O3 -std=c++14 -Wall -Wuninitialized -pedantic
+CFLAGS += -O3 -Wall -Wextra -fno-strict-aliasing
INCDIRS := \
=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -11,6 +11,7 @@ PBSEQ_BASE=/usr/include/pbseq
export LIBBLASR_INCLUDE = $(PBSEQ_BASE)/alignment
export LIBPBDATA_INCLUDE = $(PBSEQ_BASE)/pbdata
export LIBPBIHDF_INCLUDE = $(PBSEQ_BASE)/hdf
+export PBBAM_INCLUDE = $(PBSEQ_BASE)
export HDF5_LIB = /usr/lib/$(DEB_HOST_MULTIARCH)/hdf5/serial
export DALIGNER_SRC = $(CURDIR)/DALIGNER
=====================================
debian/watch
=====================================
--- a/debian/watch
+++ b/debian/watch
@@ -1,4 +1,5 @@
version=4
opts="mode=git,gitmode=full,pretty=0.3+git%cd.%h,repacksuffix=+ds,dversionmangle=s/\+ds//g,repack,compression=xz" \
- https://github.com/PacificBiosciences/pbdagcon.git HEAD
+ https://github.com/PacificBiosciences/pbdagcon.git HEAD \
+ debian debian/get-orig-source
=====================================
src/cpp/DazAlnProvider.cpp
=====================================
--- a/src/cpp/DazAlnProvider.cpp
+++ b/src/cpp/DazAlnProvider.cpp
@@ -222,7 +222,7 @@ int TargetHit::aend() {
// daligner structures.
Target::Target(): needsFree_(false) { }
-Target::Target(HITS_DB& db, int tspace, int small) :
+Target::Target(DAZZ_DB& db, int tspace, int small) :
db_(db),
tspace_(tspace),
small_(small),
=====================================
src/cpp/DazAlnProvider.hpp
=====================================
--- a/src/cpp/DazAlnProvider.hpp
+++ b/src/cpp/DazAlnProvider.hpp
@@ -94,7 +94,7 @@ std::ostream& operator<<(std::ostream& ostrm, TargetHit& hit);
class Target {
public:
Target();
- Target(HITS_DB& db, int tspace, int small);
+ Target(DAZZ_DB& db, int tspace, int small);
~Target();
// Initializes this target based on the given record, possibly scoring as
@@ -119,7 +119,7 @@ public:
std::vector<TargetHit> hits;
private:
- HITS_DB db_;
+ DAZZ_DB db_;
char* abuffer_, *bbuffer_;
Work_Data* work_;
int tspace_, small_;
@@ -158,7 +158,7 @@ private:
const ProgramOpts popts_;
// Dazzler-related data
- HITS_DB db_;
+ DAZZ_DB db_;
int64 novl_, covl_;
int tbytes_;
FILE* input_;
=====================================
src/cpp/makefile
=====================================
--- a/src/cpp/makefile
+++ b/src/cpp/makefile
@@ -8,7 +8,7 @@ PBDAGCON_OBJECTS := BlasrM5AlnProvider.o main.o SimpleAligner.o
DAZCON_OBJECTS := DB.o QV.o align.o DazAlnProvider.o dazcon.o
CPPFLAGS += -MMD -MP
-CXXFLAGS = -O3 -std=c++11 -Wall -Wuninitialized -pedantic
+CXXFLAGS = -O3 -std=c++14 -Wall -Wuninitialized -pedantic
CFLAGS = -O3 -Wall -Wextra -fno-strict-aliasing
INCDIRS := \
@@ -18,8 +18,7 @@ INCDIRS := \
${LIBPBDATA_INCLUDE} \
${LIBPBIHDF_INCLUDE} \
${PBBAM_INCLUDE} \
- ${HDF5_INCLUDE} \
- ${HTSLIB_INCLUDE}
+ ${HDF5_INCLUDE}
SYS_INCDIRS := \
${BOOST_INCLUDE} \
${THISDIR}/third-party
@@ -29,7 +28,6 @@ LIBDIRS := \
${LIBPBIHDF_LIB} \
${PBBAM_LIB} \
${HDF5_LIB} \
- ${HTSLIB_LIB} \
${GCC_LIB} \
${ZLIB_LIB}
LDLIBS+= \
@@ -38,11 +36,11 @@ LDLIBS+= \
${LIBPBIHDF_LIBFLAGS} \
${PBBAM_LIBFLAGS} \
${HDF5_LIBFLAGS} \
- ${HTSLIB_LIBFLAGS} \
+ ${HTSLIB_LIBS} \
${ZLIB_LIBFLAGS} \
${PTHREAD_LIBFLAGS} \
${DL_LIBFLAGS}
-CPPFLAGS+=$(patsubst %,-I%,${INCDIRS}) $(patsubst %,-isystem%,${SYS_INCDIRS})
+CPPFLAGS+=$(patsubst %,-I%,${INCDIRS}) $(patsubst %,-isystem%,${SYS_INCDIRS}) $(HTSLIB_CFLAGS)
LDFLAGS+=$(patsubst %,-L %,${LIBDIRS})
LDFLAGS += ${EXTRA_LDFLAGS}
=====================================
src/filterm4.py
=====================================
--- a/src/filterm4.py
+++ b/src/filterm4.py
@@ -3,6 +3,7 @@
# Filters for unique, highest scoring subread query/target pairs from an m4
# file. Helps get rid of chimeras, at the cost of some yield.
+from __future__ import print_function
import sys
from collections import namedtuple
@@ -36,7 +37,7 @@ def printUniq(qgroup, count):
for r in top.values():
count.filt += 1
- print r,
+ print(r, end=' ')
qgroup[:] = []
=====================================
src/m4topre.py
=====================================
--- a/src/m4topre.py
+++ b/src/m4topre.py
@@ -2,6 +2,7 @@
"""Super-simple converter from blasr m4 alignments to pbdagcon 'pre'
alignments. For use in the pre-assembler dagcon workflow.
"""
+from __future__ import print_function
import sys
import heapq
@@ -201,8 +202,8 @@ def main(): # pylint: disable=R0914
else:
tseq = seqs[rec.tname].translate(__rc__)[::-1][tst:tnd]
- print ' '.join([rec.qname, rec.tname, strand,
- rec.tseqlength, str(tst), str(tnd), qseq, tseq])
+ print(' '.join([rec.qname, rec.tname, strand,
+ rec.tseqlength, str(tst), str(tnd), qseq, tseq]))
if __name__ == '__main__':
sys.exit(main())
=====================================
src/q-sense.py
=====================================
--- a/src/q-sense.py
+++ b/src/q-sense.py
@@ -1,4 +1,5 @@
#!/usr/bin/env python
+from __future__ import print_function
import sys
import os
import logging
@@ -85,8 +86,8 @@ class Consensus(PBMultiToolRunner):
prefix = ".".join(prefix)
full_prefix = os.path.join(self.args.out_dir_name, prefix)
with open("%s_ref.fa" % full_prefix, "w") as f:
- print >>f ,">%s_ref" % self.args.consensus_seq_name
- print >>f, s
+ print(">%s_ref" % self.args.consensus_seq_name, file=f)
+ print(s, file=f)
hp_corr = True if self.args.enable_hp_corr else False
mark_lower_case = True if self.args.mark_lower_case else False
generate_consensus(input_fasta_name, "%s_ref.fa" % full_prefix, full_prefix, self.args.consensus_seq_name,
=====================================
test/cpp/makefile
=====================================
--- a/test/cpp/makefile
+++ b/test/cpp/makefile
@@ -15,7 +15,6 @@ INCDIRS := . \
${LIBPBIHDF_INCLUDE} \
${PBBAM_INCLUDE} \
${HDF5_INCLUDE} \
- ${HTSLIB_INCLUDE} \
${BOOST_INCLUDE} \
${GTEST_INCLUDE} \
third-party
@@ -26,7 +25,6 @@ LIBDIRS := \
${LIBPBIHDF_LIB} \
${PBBAM_LIB} \
${HDF5_LIB} \
- ${HTSLIB_LIB} \
${GCC_LIB} \
${ZLIB_LIB}
@@ -37,11 +35,11 @@ LDLIBS+= \
${LIBPBIHDF_LIBFLAGS} \
${PBBAM_LIBFLAGS} \
${HDF5_LIBFLAGS} \
- ${HTSLIB_LIBFLAGS} \
+ ${HTSLIB_LIBS} \
${ZLIB_LIBFLAGS} \
${PTHREAD_LIBFLAGS} \
${DL_LIBFLAGS}
-CPPFLAGS+=$(patsubst %,-I%,${INCDIRS})
+CPPFLAGS+=$(patsubst %,-I%,${INCDIRS}) $(HTSLIB_CFLAGS)
LDFLAGS+=$(patsubst %,-L %,${LIBDIRS})
# For fused-src, gtest-all.cc includes gtest/*.
@@ -50,7 +48,7 @@ LDFLAGS+=$(patsubst %,-L %,${LIBDIRS})
GTEST_CPPFLAGS += -isystem $(GTEST_INCLUDE) -isystem ${GTEST_SRC}/..
GTEST_CXXFLAGS += -g -Wall -Wextra -pthread
-CXXFLAGS := -O3 -std=c++11
+CXXFLAGS := -O3 -std=c++14
GTEST_OBJECTS := gtest-all.o gtest_main.o
DAZCON_OBJECTS := DB.o QV.o align.o Alignment.o \
View it on GitLab: https://salsa.debian.org/med-team/pbdagcon/compare/439fc65a84f142570223a477914d403ece9f2354...7444cf1a66f4e8fc00a67295f87cac52c5656d56
--
View it on GitLab: https://salsa.debian.org/med-team/pbdagcon/compare/439fc65a84f142570223a477914d403ece9f2354...7444cf1a66f4e8fc00a67295f87cac52c5656d56
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20180816/74fa9a18/attachment-0001.html>
More information about the debian-med-commit
mailing list