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#!/usr/bin/make -f
# This package is maintained by the Debian Med packaging team. Please refer to
# our group policy if you would like to commit to our Git repository. All
# Debian developpers have write acces to it.
#
# https://med-team.pages.debian.net/policy/
include /usr/share/dpkg/default.mk
prefix=$(CURDIR)/debian/$(DEB_SOURCE)/usr
mandir=$(prefix)/share/man/man1
libexecdir=$(prefix)/lib/$(DEB_SOURCE)
# Copy and extend upstream CXXFLAGS here because makefile enables only overriding them
export DEB_CXXFLAGS_MAINT_APPEND += -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3
export DEB_CPPFLAGS_MAINT_APPEND += -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP
# -Wconversion
# -fomit-frame-pointer ?
export DEB_LDFLAGS_MAINT_APPEND += -pthread
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
# Ensure the COMMAND-plain variants is used to generate the manpages
# for reproducible builds
export SIMD_LIST = fallback-to-plain-simd
export LC_ALL=C.UTF-8
export LANG=C.UTF-8
BUILT_USING=$(shell dpkg-query -f '$${source:Package} (= $${source:Version}), ' -W "libsimde-dev")
%:
dh $@
override_dh_auto_build:
ifeq (amd64,$(DEB_HOST_ARCH))
mkdir -p $(prefix)
mkdir -p $(libexecdir)
for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \
dh_auto_build -- all SFX=-$${SIMD} CFLAGS="$(CFLAGS) -m$${SIMD}" CXXFLAGS="$(CXXFLAGS) -m$${SIMD}" ; \
find . -name '*.o' -delete ; \
find . -name '*.o5' -delete ; \
done
dh_auto_build -- all SFX=-plain CFLAGS="$(CFLAGS)" CXXFLAGS="$(CXXFLAGS)"
else ifeq (i386,$(DEB_HOST_ARCH))
mkdir -p $(prefix)
mkdir -p $(libexecdir)
for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 sse; do \
dh_auto_build -- all SFX=-$${SIMD} CFLAGS="$(CFLAGS) -m$${SIMD}" CXXFLAGS="$(CXXFLAGS) -m$${SIMD}" ; \
find . -name '*.o' -delete ; \
find . -name '*.o5' -delete ; \
done
dh_auto_build -- all SFX=-plain CFLAGS="$(CFLAGS)" CXXFLAGS="$(CXXFLAGS)"
else
dh_auto_build
endif
HELP2MAN = help2man --no-info --version-string="$(DEB_VERSION_UPSTREAM)"
override_dh_auto_install:
ifeq (amd64,$(DEB_HOST_ARCH))
dh_install debian/bin/simd-dispatch /usr/lib/$(DEB_SOURCE)/
dh_install bin/lastdb-* bin/lastal-* bin/last-split-* bin/last-merge-batches-* bin/last-pair-probs-* usr/lib/last-align
dh_install bin/fastq-* bin/fasta-* bin/last-dotplot bin/last-map-probs bin/last-postmask bin/last-train bin/maf-* bin/parallel-fast* usr/bin
mkdir -p $(prefix)/bin
cd $(prefix)/bin \
&& for prog in lastdb lastal last-split last-merge-batches last-pair-probs ; do \
ln -s ../lib/$(DEB_SOURCE)/simd-dispatch $${prog} ; done
else ifeq (i386,$(DEB_HOST_ARCH))
dh_install debian/bin/simd-dispatch /usr/lib/$(DEB_SOURCE)/
dh_install bin/lastdb-* bin/lastal-* bin/last-split-* bin/last-merge-batches-* bin/last-pair-probs-* usr/lib/last-align
dh_install bin/fastq-* bin/fasta-* bin/last-dotplot bin/last-map-probs bin/last-postmask bin/last-train bin/maf-* bin/parallel-fast* usr/bin
mkdir -p $(prefix)/bin
cd $(prefix)/bin \
&& for prog in lastdb lastal last-split last-merge-batches last-pair-probs ; do \
ln -s ../lib/$(DEB_SOURCE)/simd-dispatch $${prog} ; done
else
$(MAKE) -j$(NUMJOBS) install prefix=$(prefix)
endif
override_dh_auto_clean:
ifeq (amd64,$(DEB_HOST_ARCH))
for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \
dh_auto_clean -- SFX=-$${SIMD} ; done
else ifeq (i386,$(DEB_HOST_ARCH))
for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 sse plain; do \
dh_auto_clean -- SFX=-$${SIMD} ; done
else
dh_auto_clean
endif
for i in last-merge-batches last-pair-probs last-split lastal lastdb ; \
do \
for j in avx avx2 plain sse2 sse3 sse4.1 ssse3 sse3 sse2 sse ; \
do \
rm -f bin/$$i-$$j ; \
done ; \
done
override_dh_installman:
dh_installman
$(HELP2MAN) \
--name='make a dotplot, a.k.a. Oxford Grid, of alignments in LAST tabular format' \
$(CURDIR)/bin/last-dotplot > $(mandir)/last-dotplot.1
$(HELP2MAN) \
--name="genome-scale comparison of biological sequences" \
--help-option="-h" \
$(prefix)/bin/lastal > $(mandir)/lastal.1
# help2man output needs manual postprocessing - see debian/mans
#$(HELP2MAN) \
# --name="genome-scale comparison of biological sequences" \
# --help-option="-h" \
# $(prefix)/bin/lastdb > $(mandir)/lastdb.1
$(HELP2MAN) \
--name="Sort MAF-format alignments by sequence name" \
$(CURDIR)/bin/maf-sort > $(mandir)/maf-sort.1
$(HELP2MAN) \
--name="changes the order of the sequences in MAF-format alignments" \
$(CURDIR)/bin/maf-swap > $(mandir)/maf-swap.1
# help2man output needs manual postprocessing - see debian/mans
#$(HELP2MAN) \
# --name="Add extra column with mapping probabilities" \
# $(CURDIR)/bin/last-map-probs > $(mandir)/last-map-probs.1
# This script has not enough to put in a manual page.
#$(HELP2MAN) \
# --name="Read files of lastal output, merge corresponding batches, and write them." \
# $(CURDIR)/bin/last-merge-batches > $(mandir)/last-merge-batches.1
# # These bin were droped
#$(HELP2MAN) \
# --name="Clean up MAF-format alignments" \
# $(CURDIR)/bin/last-reduce-alignments > $(mandir)/last-reduce-alignments.1
#$(HELP2MAN) \
# --name='Remove MAF-format alignments which are "dominated" by others' \
# $(CURDIR)/bin/last-remove-dominated > $(mandir)/last-remove-dominated.1
$(HELP2MAN) \
--name='Estimates "split" or "spliced" alignments.' \
$(prefix)/bin/last-split > $(mandir)/last-split.1
$(HELP2MAN) \
--name="Join two or more sets of MAF-format multiple alignments" \
$(CURDIR)/bin/maf-join > $(mandir)/maf-join.1
$(HELP2MAN) \
--help-option="-h" \
$(CURDIR)/bin/maf-cut > $(mandir)/maf-cut.1
$(HELP2MAN) \
--name="Convert MAF-format alignments to tabular format" \
$(CURDIR)/bin/maf-convert > $(mandir)/maf-convert.1
$(HELP2MAN) \
--name="Read 2 fastq files, and write them interleaved" \
$(CURDIR)/bin/fastq-interleave > $(mandir)/fastq-interleave.1
$(HELP2MAN) \
--name="Read files of lastal output, merge corresponding batches, and write them" \
$(prefix)/bin/last-merge-batches > $(mandir)/last-merge-batches.1
# help2man output needs manual postprocessing - see debian/mans
#$(HELP2MAN) \
# --name="Read alignments of paired DNA reads to a genome, and do estimations" \
# $(prefix)/bin/last-pair-probs > $(mandir)/last-pair-probs.1
$(HELP2MAN) \
--name="Get alignments that have a segment with score >= threshold, with gentle masking of lowercase letters" \
$(CURDIR)/bin/last-postmask > $(mandir)/last-postmask.1
$(HELP2MAN) \
--name="Try to find suitable score parameters for aligning the given sequences" \
$(CURDIR)/bin/last-train > $(mandir)/last-train.1
$(HELP2MAN) \
--name="Keep the first of identical sequences" \
--help-option="-h" \
$(prefix)/bin/fasta-nr > $(mandir)/fasta-nr.1
override_dh_gencontrol:
dh_gencontrol -- -VBuilt-Using="$(BUILT_USING)"
|
