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|
#!/usr/bin/make -f
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
include /usr/share/dpkg/default.mk
mandir := $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/man/man1
utildir := $(CURDIR)/build/util
bindir := $(CURDIR)/build/src
include /usr/share/dpkg/architecture.mk
HELP2MAN = /usr/bin/help2man --no-info --version-string=${DEB_VERSION}
export DEB_CFLAGS_MAINT_APPEND=-O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration
# -Werror=implicit-function-declaration is to catch issues with SIMD levels
%:
dh $@ --builddir build
override_dh_auto_configure:
rm -Rf src/simde
ifeq (amd64,$(DEB_HOST_ARCH))
# TODO: redo this based upon the amd64 micro-architectural levels; x86-64-v3 includes BMI1 BMI2 LZCNT, etc..
DEB_CFLAGS_MAINT_APPEND="${DEB_CFLAGS_MAINT_APPEND} -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI" dh_auto_configure --reload-all-buildenv-variables -- --with-gmapdb=/var/cache/gmap \
--bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse2
DEB_CFLAGS_MAINT_APPEND="${DEB_CFLAGS_MAINT_APPEND} -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI" dh_auto_configure --reload-all-buildenv-variables --builddir build_ssse3 -- --with-gmapdb=/var/cache/gmap \
--bindir=/usr/lib/gmap --enable-simd --with-simd-level=ssse3 ax_cv_cpu_has_ssse3_ext=yes ax_cv_compile_ssse3_ext=yes ax_cv_link_tmmintrin_h=yes
DEB_CFLAGS_MAINT_APPEND="${DEB_CFLAGS_MAINT_APPEND} -UHAVE_STTNI" dh_auto_configure --builddir build_sse41 -- --with-gmapdb=/var/cache/gmap \
--bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse41 ax_cv_cpu_has_sse41_ext=yes ax_cv_compile_sse41_ext=yes ax_cv_link_smmintrin_h=yes
dh_auto_configure --builddir build_sse42 -- --with-gmapdb=/var/cache/gmap \
--bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse42 ax_cv_cpu_has_sse42_ext=yes ax_cv_compile_sse42_ext=yes ax_cv_link_nmmintrin_h=yes ax_cv_cpu_has_popcnt_ext=yes ax_make_sse42=yes ax_cv_cpu_has_bmi1_ext=yes ax_cv_compile_bmi_ext=yes ax_cv_link_bmi=yes
dh_auto_configure --builddir build_avx2 -- --with-gmapdb=/var/cache/gmap \
--bindir=/usr/lib/gmap --enable-simd --with-simd-level=avx2 ax_make_avx2=yes ax_cv_cpu_has_bmi2_ext=yes ax_cv_compile_bmi2_ext=yes ax_cv_link_bmi2=yes
dh_auto_configure --builddir build_avx512 -- --with-gmapdb=/var/cache/gmap \
--bindir=/usr/lib/gmap --enable-simd --with-simd-level=avx512 ax_cv_cpu_has_avx512_ext=yes ax_cv_compile_avx512_ext=yes ax_cv_compile_avx512bw_ext=no ax_cv_link_avx512bw=no
# skipping avx512bw for now:
# ../../src/oligoindex_hr.c: In function 'count_positions_fwd_simd':
# ../../src/oligoindex_hr.c:19814:3: error: 'hugereverse8' undeclared (first use in this function); did you mean 'bigreverse8'?
# 19814 | hugereverse8 = _mm512_broadcast_i64x4(bigreverse8);
# | ^~~~~~~~~~~~
# | bigreverse8
else
dh_auto_configure -- --with-gmapdb=/var/cache/gmap \
--bindir=/usr/lib/gmap --disable-simd
endif
override_dh_auto_build:
dh_auto_build
ifeq (amd64,$(DEB_HOST_ARCH))
dh_auto_build --builddir build_ssse3
dh_auto_build --builddir build_sse41
dh_auto_build --builddir build_sse42
dh_auto_build --builddir build_avx2
dh_auto_build --builddir build_avx512
endif
override_dh_auto_install:
mkdir -p $(mandir)
$(HELP2MAN) --name='Genomic Mapping and Alignment Program' \
$(bindir)/gmap |debian/filter.pl >$(mandir)/gmap.1
$(HELP2MAN) --name='Genomic Short-read Nucleotide Alignment Program' \
$(bindir)/gsnap |debian/filter.pl >$(mandir)/gsnap.1
$(HELP2MAN) --name='Large Genome Mapping and Alignment Program' \
$(bindir)/gmapl |debian/filter.pl >$(mandir)/gmapl.1
$(HELP2MAN) --name='Large Genome Short-read Nucleotide Alignment Program' \
$(bindir)/gsnapl |debian/filter.pl >$(mandir)/gsnapl.1
$(HELP2MAN) --name='Tool for genome database creation for GMAP or GSNAP' \
$(utildir)/gmap_build |debian/filter.pl >$(mandir)/gmap_build.1
ifeq (amd64,$(DEB_HOST_ARCH))
dh_auto_install --builddir build_avx512
dh_auto_install --builddir build_avx2
dh_auto_install --builddir build_sse42
dh_auto_install --builddir build_sse41
dh_auto_install --builddir build_ssse3
endif
dh_auto_install
override_dh_install:
mkdir -p debian/$(DEB_SOURCE)/usr/bin
dh_install
for bin in `echo gmap gsnap gmap_build gmapl gsnapl; \
cd $(CURDIR)/debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/; \
ls -1 gmap*.* gsnap*.* `; do \
ln -s /usr/lib/gmap/$$bin debian/$(DEB_SOURCE)/usr/bin/$$bin; \
done
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
dh_auto_test --no-parallel
endif
override_dh_auto_clean:
ifeq (amd64,$(DEB_HOST_ARCH))
dh_auto_clean --builddir build_avx512
dh_auto_clean --builddir build_avx2
dh_auto_clean --builddir build_sse42
dh_auto_clean --builddir build_sse41
dh_auto_clean --builddir build_ssse3
endif
dh_auto_clean
override_dh_installexamples:
mkdir $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/examples
find tests/ -type f -print0 | xargs -0r sed -i \
-e 's@$(CURDIR)@«buildpath»@g' \
-e 's@\#! /bin/bash@\#! /bin/sh@g'
tar --sort=name \
--mtime="@${SOURCE_DATE_EPOCH}" \
--owner=root --group=root --numeric-owner \
--mode=go=rX,u+rw,a-s \
--exclude='*/align.log' \
--exclude='*/Makefile' \
--exclude='*/Makefile.in' \
-cJf $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/examples/tests.tar.xz tests
|
