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commit 153c0f9e3efd99917ff0ada225470ec2d43a02b7 Author: Afif Elghraoui <[email protected]> Date: Tue Nov 1 00:24:19 2016 -0700 build bax2bam and bam2bax These two programs have their own build systems, so somewhat complicate the packaging. bam2bax in particular requires pbseqlib to be compiled with pbbam. --- debian/TODO | 2 +- debian/control | 2 ++ debian/install | 2 ++ debian/patches/cmake-utils.patch | 25 +++++++++++++++++++++++ debian/patches/disable-gtest.patch | 28 +++++++++++++++++++++++++ debian/patches/series | 2 ++ debian/rules | 42 ++++++++++++++++++++++++++++++++------ 7 files changed, 96 insertions(+), 7 deletions(-) diff --git a/debian/TODO b/debian/TODO index 04d3e21..7139ddb 100644 --- a/debian/TODO +++ b/debian/TODO @@ -2,4 +2,4 @@ * Update manpages -* build bax2bam and bam2bax +* run test suite for bax2bam and bam2bax diff --git a/debian/control b/debian/control index 3aa10bd..5c0f3b5 100644 --- a/debian/control +++ b/debian/control @@ -6,6 +6,8 @@ Uploaders: Afif Elghraoui <[email protected]> Build-Depends: debhelper (>= 9), python, + cmake, + libboost-dev, libhdf5-dev, zlib1g-dev, libpbseq-dev (>= 0~20160912), diff --git a/debian/install b/debian/install index 5bc54f4..35c29dc 100644 --- a/debian/install +++ b/debian/install @@ -7,3 +7,5 @@ utils/samFilter usr/bin utils/toAfg usr/bin utils/sawriter usr/bin utils/sdpMatcher usr/bin +utils/bax2bam/bin/* usr/bin +utils/bam2bax/bin/* usr/bin diff --git a/debian/patches/cmake-utils.patch b/debian/patches/cmake-utils.patch new file mode 100644 index 0000000..1bb56da --- /dev/null +++ b/debian/patches/cmake-utils.patch @@ -0,0 +1,25 @@ +Description: Fix passage of boost header paths to cmake +Author: Afif Elghraoui <[email protected]> +Forwarded: no +--- blasr.orig/utils/bax2bam/makefile ++++ blasr/utils/bax2bam/makefile +@@ -7,7 +7,7 @@ + all: ${CURDIR}/src/* ${CURDIR}/tests/src/* + @mkdir -p ${CURDIR}/build && \ + cd ${CURDIR}/build && \ +- cmake -DBOOST_ROOT=${BOOST_ROOT} \ ++ cmake -DBoost_INCLUDE_DIRS=${BOOST_INC} \ + -DPacBioBAM_INCLUDE_DIRS=${PBBAM_INC} \ + -DHTSLIB_INCLUDE_DIRS=${HTSLIB_INC} \ + -DPacBioBAM_LIBRARIES=${PBBAM_LIB}/libpbbam${SH_LIB_EXT} \ +--- blasr.orig/utils/bam2bax/makefile ++++ blasr/utils/bam2bax/makefile +@@ -7,7 +7,7 @@ + all: ${CURDIR}/src/*.cpp ${CURDIR}/src/*.h ${CURDIR}/tests/src/*.cpp ${CURDIR}/tests/src/*.h + @mkdir -p ${CURDIR}/build && \ + cd ${CURDIR}/build && \ +- cmake -DBOOST_ROOT=${BOOST_ROOT} \ ++ cmake -DBoost_INCLUDE_DIRS=${BOOST_INC} \ + -DPacBioBAM_INCLUDE_DIRS=${PBBAM_INC} \ + -DHTSLIB_INCLUDE_DIRS=${HTSLIB_INC} \ + -DPacBioBAM_LIBRARIES=${PBBAM_LIB}/libpbbam${SH_LIB_EXT} \ diff --git a/debian/patches/disable-gtest.patch b/debian/patches/disable-gtest.patch new file mode 100644 index 0000000..548b0fd --- /dev/null +++ b/debian/patches/disable-gtest.patch @@ -0,0 +1,28 @@ +Description: temporarily disable gtests for bax2bam and bam2bax + We should make use of the packaged gtest; without additional effort, + the build system doesn't find it. +Author: Afif Elghraoui <[email protected]> +Forwarded: not-needed +Last-Update: 2016-12-20 +--- blasr.orig/utils/bam2bax/CMakeLists.txt ++++ blasr/utils/bam2bax/CMakeLists.txt +@@ -14,7 +14,7 @@ + ) + + # build-time options +-option(Bam2Bax_build_tests "Build Bam2Bax's unit tests." ON) ++option(Bam2Bax_build_tests "Build Bam2Bax's unit tests." OFF) + + # main project paths + set(Bam2Bax_RootDir ${Bam2Bax_SOURCE_DIR}) +--- blasr.orig/utils/bax2bam/CMakeLists.txt ++++ blasr/utils/bax2bam/CMakeLists.txt +@@ -14,7 +14,7 @@ + ) + + # build-time options +-option(Bax2BAM_build_tests "Build Bax2BAM's unit tests." ON) ++option(Bax2BAM_build_tests "Build Bax2BAM's unit tests." OFF) + + # main project paths + set(Bax2Bam_RootDir ${Bax2Bam_SOURCE_DIR}) diff --git a/debian/patches/series b/debian/patches/series index e69de29..0f16b2d 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -0,0 +1,2 @@ +disable-gtest.patch +cmake-utils.patch diff --git a/debian/rules b/debian/rules index eb33f93..823ec30 100755 --- a/debian/rules +++ b/debian/rules @@ -2,14 +2,26 @@ include /usr/share/dpkg/default.mk +export VERBOSE=1 # for cmake +export SH_LIB_EXT=.so + export HDF5_INC=/usr/include/hdf5/serial export HDF5_LIB=/usr/lib/$(DEB_HOST_MULTIARCH)/hdf5/serial - -PBSEQ_BASE=/usr/include/pbseq -export LIBBLASR_INC=$(PBSEQ_BASE)/alignment -export LIBPBDATA_INC=$(PBSEQ_BASE)/pbdata -export LIBPBIHDF_INC=$(PBSEQ_BASE)/hdf - +export BOOST_INC=/usr/include/boost +export HTSLIB_INC=/usr/include/htslib +export HTSLIB_LIB=/usr/lib/$(DEB_HOST_MULTIARCH) +export PBBAM_INC=/usr/include +export PBBAM_LIB=/usr/lib/$(DEB_HOST_MULTIARCH) +export PBDATA_ROOT_DIR=/usr/include/pbseq +export LIBBLASR_INC=$(PBDATA_ROOT_DIR)/alignment +export LIBBLASR_LIB=/usr/lib/$(DEB_HOST_MULTIARCH) +export LIBPBDATA_INC=$(PBDATA_ROOT_DIR)/pbdata +export LIBPBDATA_LIB=/usr/lib/$(DEB_HOST_MULTIARCH) +export LIBPBIHDF_INC=$(PBDATA_ROOT_DIR)/hdf +export LIBPBIHDF_LIB=/usr/lib/$(DEB_HOST_MULTIARCH) + +# CPPFLAGS apparently aren't exported for bam2bax/bax2bam +export DEB_CXXFLAGS_MAINT_PREPEND = $(CPPFLAGS) -I$(PBDATA_ROOT_DIR) %: dh $@ --parallel @@ -17,10 +29,28 @@ export LIBPBIHDF_INC=$(PBSEQ_BASE)/hdf override_dh_auto_configure: ./configure.py --shared +override_dh_auto_build: main bax2bam bam2bax; + +.PHONY: main +main: + dh_auto_build + +.PHONY: bax2bam +bax2bam: utils/bax2bax/bin/bax2bam +utils/bax2bax/bin/bax2bam: + $(MAKE) -C utils/bax2bam + +.PHONY: bam2bax +bam2bax: utils/bam2bax/bin/bam2bax +utils/bam2bax/bin/bam2bax: + $(MAKE) -C utils/bam2bax + # Tests require data not available in the source distribution override_dh_auto_test: ; override_dh_auto_clean: override_dh_auto_configure $(MAKE) clean + $(MAKE) -C utils/bam2bax clean + $(MAKE) -C utils/bax2bam clean # This is created by configure.py $(RM) defines.mk -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/blasr.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
