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last-align 963-2
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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://debian-med.alioth.debian.org/docs/policy.html

include /usr/share/dpkg/default.mk

mandir=$(CURDIR)/debian/$(DEB_SOURCE)/usr/share/man/man1/

# Copy upstream CXXFLAGS here because makefile enables only overriding them
CXXFLAGS += -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11
CPPFLAGS += -DHAS_CXX_THREADS
# -Wconversion
# -fomit-frame-pointer ?

LDFLAGS += -pthread

export DEB_BUILD_MAINT_OPTIONS = hardening=+all

%:
	dh  $@

override_dh_auto_build:
	make all CXXFLAGS="$(CXXFLAGS)" CFLAGS="$(CFLAGS)" CPPFLAGS="$(CPPFLAGS)" LDFLAGS="$(LDFLAGS)"

HELP2MAN = help2man --no-info --version-string="$(DEB_VERSION_UPSTREAM)"

override_dh_auto_install:
	make install prefix=$(CURDIR)/debian/$(DEB_SOURCE)/usr

override_dh_installman:
	dh_installman
	$(HELP2MAN) \
		 --name='make a dotplot, a.k.a. Oxford Grid, of alignments in LAST tabular format' \
	         $(CURDIR)/scripts/last-dotplot > $(mandir)/last-dotplot.1
	$(HELP2MAN) \
	         --name="genome-scale comparison of biological sequences" \
	         --help-option="-h" \
                 $(CURDIR)/src/lastal > $(mandir)/lastal.1
	$(HELP2MAN) \
	         --name="genome-scale comparison of biological sequences" \
	         --help-option="-h" \
                 $(CURDIR)/src/lastal8 > $(mandir)/lastal8.1
        # help2man output needs manual postprocessing - see debian/mans
	#$(HELP2MAN) \
	#         --name="genome-scale comparison of biological sequences" \
	#         --help-option="-h" \
        #         $(CURDIR)/src/lastdb > $(mandir)/lastdb.1
	$(HELP2MAN) \
                 --name="Sort MAF-format alignments by sequence name" \
                 $(CURDIR)/scripts/maf-sort > $(mandir)/maf-sort.1
	$(HELP2MAN) \
                 --name="changes the order of the sequences in MAF-format alignments" \
                 $(CURDIR)/scripts/maf-swap > $(mandir)/maf-swap.1
        # help2man output needs manual postprocessing - see debian/mans
	#$(HELP2MAN) \
        #         --name="Add extra column with mapping probabilities" \
        #         $(CURDIR)/scripts/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)/scripts/last-merge-batches > $(mandir)/last-merge-batches.1
        # These scripts were droped
	#$(HELP2MAN) \
        #         --name="Clean up MAF-format alignments" \
        #         $(CURDIR)/scripts/last-reduce-alignments > $(mandir)/last-reduce-alignments.1
	#$(HELP2MAN) \
        #         --name='Remove MAF-format alignments which are "dominated" by others' \
        #         $(CURDIR)/scripts/last-remove-dominated > $(mandir)/last-remove-dominated.1
	$(HELP2MAN) \
                 --name='Estimates "split" or "spliced" alignments.' \
                 $(CURDIR)/src/last-split > $(mandir)/last-split.1
	$(HELP2MAN) \
                 --name='Estimates "split" or "spliced" alignments.' \
                 $(CURDIR)/src/last-split8 > $(mandir)/last-split8.1
	$(HELP2MAN) \
                 --name="Join two or more sets of MAF-format multiple alignments" \
                 $(CURDIR)/scripts/maf-join > $(mandir)/maf-join.1
	$(HELP2MAN) \
                 --name="Convert MAF-format alignments to tabular format" \
                 $(CURDIR)/scripts/maf-convert > $(mandir)/maf-convert.1
	$(HELP2MAN) \
                 --name="Read 2 fastq files, and write them interleaved" \
                 $(CURDIR)/scripts/fastq-interleave > $(mandir)/fastq-interleave.1
	$(HELP2MAN) \
                 --name="Read files of lastal output, merge corresponding batches, and write them" \
                 $(CURDIR)/src/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" \
        #         $(CURDIR)/src/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)/scripts/last-postmask > $(mandir)/last-postmask.1
	$(HELP2MAN) \
                 --name="Try to find suitable score parameters for aligning the given sequences" \
                 $(CURDIR)/scripts/last-train > $(mandir)/last-train.1

override_dh_installchangelogs:
	dh_installchangelogs ChangeLog.txt