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|
#!/usr/bin/make -f
# -*- makefile -*-
include /usr/share/dpkg/architecture.mk
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
export HOME=$(CURDIR)/fakehome
NUMJOBS=1
ifneq (,$(filter parallel=%,$(DEB_BUILD_OPTIONS)))
ifneq (sh4,$(DEB_BUILD_ARCH))
NUMJOBS = $(patsubst parallel=%,%,$(filter parallel=%,$(DEB_BUILD_OPTIONS)))
endif
endif
DEB_CONFIGURE_COMMON_FLAGS=--without-autodep --without-makefile-auto-update \
--with-flat-makefile --without-caution --without-dbapi --without-lzo \
--without-debug --without-sse42
DEB_CONFIGURE_EXTRA_FLAGS=$(DEB_CONFIGURE_COMMON_FLAGS) --with-dll --with-mt \
--with-runpath=/usr/lib/ncbi-blast+ --with-build-root=BUILD \
--with-mbedtls --with-pcre2
ifneq (,$(filter amd64 arm64 x32,$(DEB_HOST_ARCH)))
VDB_SUBTREES=os/$(DEB_HOST_ARCH_OS) os/unix cc/gcc/$(DEB_HOST_GNU_CPU) cc/gcc
VDB_INC=-I/usr/include/ncbi-vdb
VDB_INCLUDE=$(VDB_INC) $(VDB_SUBTREES:%=$(VDB_INC)/%)
DEB_CONFIGURE_COMMON_FLAGS += --with-vdb=/usr VDB_INCLUDE="$(VDB_INCLUDE)"
else
DEB_CONFIGURE_COMMON_FLAGS += --without-downloaded-vdb
endif
proj=algo/blast/ app/ objmgr/ objtools/align_format/ objtools/blast/
#ifneq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS)))
DEB_CONFIGURE_EXTRA_FLAGS += --without-strip --with-symbols
#endif
#export DEB_BUILD_MAINT_OPTIONS=hardening=+all,-pie
export DEB_BUILD_MAINT_OPTIONS=hardening=+all,-pie reproducible=-timeless
export DEB_CFLAGS_MAINT_APPEND=-Wall -pedantic
ifeq ($(DEB_HOST_ARCH_BITS),32)
ifeq (,$(filter armhf %i386 x32,$(DEB_HOST_ARCH)))
export LIBS=-latomic
endif
endif
ifeq (alpha,$(DEB_HOST_ARCH))
export DEB_CFLAGS_MAINT_APPEND += -fsection-anchors
export DEB_CXXFLAGS_MAINT_APPEND += -fsection-anchors
endif
ifeq (hppa,$(DEB_HOST_ARCH))
export DEB_CFLAGS_MAINT_APPEND += -ffunction-sections
export DEB_CXXFLAGS_MAINT_APPEND += -ffunction-sections
endif
# Down to mips64el in practice, but easy enough to generalize
ifneq (,$(findstring mips,$(DEB_HOST_ARCH)))
export DEB_CFLAGS_MAINT_APPEND += -mxgot
export DEB_CXXFLAGS_MAINT_APPEND += -mxgot
endif
include /usr/share/dpkg/buildflags.mk
ifneq (,$(filter mips%,$(DEB_HOST_ARCH)))
CXXFLAGS := $(CXXFLAGS:-O%=-O)
DEB_CONFIGURE_EXTRA_FLAGS += FAST_CXXFLAGS=-O
endif
ifeq (sh4,$(DEB_HOST_ARCH))
DEB_CONFIGURE_COMMON_FLAGS += --without-optimization
endif
export CFLAGS CPPFLAGS CXXFLAGS LDFLAGS MAKE
# used for run_with_lock
DEB_CONFIGURE_COMMON_FLAGS += CFLAGS_FOR_BUILD="$(CFLAGS) -fPIE"
DEB_CONFIGURE_COMMON_FLAGS += LDFLAGS_FOR_BUILD="$(LDFLAGS)"
ifneq ($(DEB_BUILD_ARCH),$(DEB_HOST_ARCH))
NATIVE=.native
DEB_CONFIGURE_EXTRA_FLAGS += --build=$(DEB_BUILD_GNU_TYPE) \
--host=$(DEB_HOST_GNU_TYPE)
NATIVE_BINDIR=$(CURDIR)/c++/BUILD$(NATIVE)/bin
PREBUILT_DATATOOL_EXE=$(NATIVE_BINDIR)/datatool
PREBUILT_PTB_EXE=$(NATIVE_BINDIR)/project_tree_builder
export PREBUILT_DATATOOL_EXE PREBUILT_PTB_EXE
$(PREBUILT_DATATOOL_EXE):
cd c++ && PREBUILT_PTB_EXE=bootstrap \
./configure $(DEB_CONFIGURE_COMMON_FLAGS) --without-objects \
--without-algo --without-app --with-build-root=BUILD.native || \
(tail -v -n +0 config.log BUILD.native/status/config.log; exit 1)
make -j$(NUMJOBS) -C c++/BUILD$(NATIVE)/build -f Makefile.flat \
datatool.exe
endif
override_dh_autoreconf:
cd c++ && \
autoheader2.69 -Isrc/build-system src/build-system/configure.ac \
&& cd src/build-system && autoconf2.69
override_dh_auto_configure-indep:;
override_dh_auto_configure-arch: $(PREBUILT_DATATOOL_EXE)
mkdir -p $(HOME)
cd c++ && CONFIG_SHELL=/bin/bash \
./configure $(DEB_CONFIGURE_EXTRA_FLAGS) \
|| (tail -v -n +0 config.log BUILD/status/config.log; exit 1)
override_dh_auto_build-arch:
cd c++/BUILD/build && \
make -j$(NUMJOBS) -f Makefile.flat all_projects="$(proj)"
# make all_r
override_dh_auto_build-indep:
echo "Save time and do nothing for architecture independent builds"
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
-dh_auto_test
-c++/BUILD/build/check.sh concat_err
-cat c++/BUILD/build/check.sh.out_err
endif
instroot = debian/ncbi-blast+/usr
leg_bin = debian/ncbi-blast+-legacy/usr/bin
override_dh_auto_install-arch:
# cp c++/BUILD/lib/*.so $(instroot)/lib/ncbi-blast+/
cp c++/BUILD/bin/* $(instroot)/bin/
override_dh_auto_install-indep:
echo "Nothing to do for architecture independant installs"
override_dh_install-arch:
# dh_install
mv $(instroot)/bin/rpsblast $(instroot)/bin/rpsblast+
mv $(instroot)/bin/seedtop $(instroot)/bin/seedtop+
mv $(instroot)/bin/get_species_taxids.sh \
$(instroot)/bin/get_species_taxids
mv $(instroot)/bin/cleanup-blastdb-volumes.py \
$(instroot)/bin/cleanup-blastdb-volumes
mv $(instroot)/bin/legacy_blast.pl $(instroot)/bin/legacy_blast
mv $(instroot)/bin/update_blastdb.pl $(instroot)/bin/update_blastdb
sed -e '1s/$$/3/' $(instroot)/bin/windowmasker_2.2.22_adapter.py \
> $(instroot)/bin/windowmasker_2.2.22_adapter
chmod +x $(instroot)/bin/windowmasker_2.2.22_adapter
rm $(instroot)/bin/windowmasker_2.2.22_adapter.py*
# Clean up tests, demos, and internal build tools
rm -f $(instroot)/bin/*test* $(instroot)/bin/seqdb_demo \
$(instroot)/bin/datatool $(instroot)/bin/run_with_lock \
$(instroot)/bin/project_tree_builder
mkdir c++/BUILD/lib.observed
d=$(instroot)/bin; \
while :; do \
(for x in $$d/*; do \
readelf -d $$x 2>/dev/null \
| sed -ne 's/.*NEEDED.* \[\(.*\)]$$/\1/p'; \
done; rm -f c++/BUILD/lib.observed/*) | sort -u | while read l; do \
[ -f $(instroot)/lib/ncbi-blast+/$$l \
-o \! -f c++/BUILD/lib/$$l ] || \
cp -av c++/BUILD/lib/$$l c++/BUILD/lib.observed/; \
done; \
[ -n "$$(ls c++/BUILD/lib.observed)" ] || break; \
echo ------------------------------------------------------------; \
cp -a c++/BUILD/lib.observed/* $(instroot)/lib/ncbi-blast+; \
d=c++/BUILD/lib.observed; \
done
override_dh_install-indep:
#if test -d $(leg_bin); then cp debian/legacy/legacy.sh $(leg_bin)/; fi
for x in blastall megablast blastpgp bl2seq rpsblast fastacmd formatdb \
seedtop; do \
sed -e "s/.{.*}/$$x/" debian/legacy/legacy.sh > $(leg_bin)/$$x; \
chmod +x $(leg_bin)/$$x; \
done
NEW_MODULE = $(CURDIR)/c++/BUILD$(NATIVE)/build/new_module.sh
override_dh_clean:
cp c++/src/util/lmdb/Makefile.orig c++/src/util/lmdb/Makefile.orig.save
cp c++/src/util/lmdbxx/Makefile.orig c++/src/util/lmdbxx/Makefile.orig.save
cp c++/src/util/lmdbxx/lmdb++.h.orig c++/src/util/lmdbxx/lmdb++.h.orig.save
cp c++/configure.orig configure.orig.save
dh_clean
#Tricky - for each module directory there may be several module files
#or there may be none but then there is still a module named after the
#directory. Clean everything!
-for x in c++/src/objects/* ; do \
(cd "$$x" && ( \
mods="`echo *.module`" ; \
[ "$${mods#*\*}" = "$$mods" ] || mods="`basename $$x`" ; \
for mod in $$mods ; do \
$(NEW_MODULE) $$mod purge_sources ; \
done ) ; \
) ; \
done
-for x in c++/src/objtools/eutils/* ; do \
(cd "$$x" && ( \
mods="`echo *.module`" ; \
[ "$${mods#*\*}" = "$$mods" ] || mods="`basename $$x`" ; \
for mod in $$mods ; do \
$(NEW_MODULE) --dtd $$mod purge_sources ; \
done ) ; \
) ; \
done
-cd c++/src/objtools/eutils/efetch && \
$(NEW_MODULE) --xsd efetch purge_sources
rm -rf c++/compilers/dll c++/config.log c++/Makefile
rm -f c++/configure.lineno c++/src/objects/blastxml/blastxml.module
rm -f c++/include/common/ncbi_revision.h
find -name check_exec.pid -delete
rm -rf c++/BUILD c++/BUILD.native fakehome
mv configure.orig.save c++/configure.orig
mv c++/src/util/lmdb/Makefile.orig.save c++/src/util/lmdb/Makefile.orig
mv c++/src/util/lmdbxx/Makefile.orig.save c++/src/util/lmdbxx/Makefile.orig
mv c++/src/util/lmdbxx/lmdb++.h.orig.save c++/src/util/lmdbxx/lmdb++.h.orig
%:
dh $@ --sourcedirectory=c++ --with-autoreconf
|
