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|
#!/usr/bin/make -f
export DH_VERBOSE=1
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
# TODO - migrate all binary JARs to use the packaged versions instead.
# activation.jar never used?? Or sould we use the system version?
# Note activation.jar was included in upstream but unused.
#export CLASSPATH=/usr/share/java/activation.jar:
%:
dh $@
include /usr/share/dpkg/default.mk
VERSION=$(DEB_VERSION_UPSTREAM)
RENAMED := cons pscan
# Disable java packages on architecture that don't have
# an openjdk port.
nojava_archs = hppa
ifneq (,$(filter $(DEB_HOST_ARCH), $(nojava_archs)))
export DEB_BUILD_PROFILES += nojava
endif
EMBOSS-TMP = $(CURDIR)/debian/emboss_tmp
EMBOSS = $(CURDIR)/debian/emboss
EMBOSS-TEST = $(CURDIR)/debian/emboss-test
EMBOSS-LIB = $(CURDIR)/debian/emboss-lib
CONFFLAGS = --bindir=/usr/lib/emboss
CONFFLAGS += --libdir=/usr/lib/emboss/lib
CONFFLAGS += --includedir=/usr/lib/emboss/include
CONFFLAGS += --enable-systemlibs
ifeq ($(filter nojava,$(DEB_BUILD_PROFILES)),)
CONFFLAGS += --with-java=/usr/lib/jvm/default-java/include
CONFFLAGS += --with-javaos=/usr/lib/jvm/default-java/include/linux
endif
CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
CFLAGS:=$(shell dpkg-buildflags --get CFLAGS)
DEB_LDFLAGS += -lexpat
DEB_LDFLAGS += $(shell mysql_config --libs)
DEB_LDFLAGS += -lpq
DEB_LDFLAGS += $(shell dpkg-buildflags --get LDFLAGS)
#DEB_LDFLAGS += $(shell pg_config | grep LIBS | cut -f2 -d=)
override_dh_auto_configure:
dh_auto_configure -- $(CONFFLAGS)
override_dh_auto_build:
dh_auto_build -- AJAX_FIXED_ROOT=\\\"/usr/share/EMBOSS\\\" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" LDFLAGS="$(DEB_LDFLAGS)"
ifeq ($(filter nojava,$(DEB_BUILD_PROFILES)),)
# Add 2 extra files wanted in jemboss.jar
cd jemboss/lib && make jemboss.jar
cd jemboss && jar uf lib/jemboss.jar resources/version resources/*.properties
endif
override_dh_clean:
rm -rf debian/emboss_tmp
find jemboss/ -type f -name "*.class" -delete
[ ! -d debian/testbackup ] || ( $(RM) --recursive test ; mv debian/testbackup test )
dh_clean --exclude=feattext.html~ config.status test-stamp install-stamp
rm -f jemboss/runJemboss.sh
rm -f jemboss/utils/makeJar.csh
rm -f jemboss/lib/jemboss.jar jemboss/resources/resources.jar jemboss/lib/activation.jar
find test '(' -name 'Makefile' -o -name 'Makefile.in' ')' -delete
rm -f config.guess
override_dh_auto_install-arch:
### Binaries and data go to a temporary dir before being moved to their own package ###
$(MAKE) -C emboss install DESTDIR=$(EMBOSS-TMP)
# Make symbolic links from /usr/bin to /usr/lib/emboss
cd $(EMBOSS)/usr/bin/ ; \
for i in $(EMBOSS-TMP)/usr/lib/emboss/* ; \
do ln -sf ../lib/emboss/`basename $$i` . ; \
done
### Renaming conflicting binaries (see also in binary-arch) ###
for i in $(RENAMED) ; \
do mv $(EMBOSS)/usr/bin/$$i $(EMBOSS)/usr/bin/em_$$i ; \
done
### EMBOSS libraries go in the emboss-lib package. ###
$(MAKE) -C ajax install DESTDIR=$(EMBOSS-LIB)
$(MAKE) -C nucleus install DESTDIR=$(EMBOSS-LIB)
$(MAKE) -C plplot install DESTDIR=$(EMBOSS-LIB)
find $(EMBOSS-LIB)/usr/lib -name '*.la' -exec rm {} \;
### Documentation goes in emboss-doc. ###
$(MAKE) -C doc install DESTDIR=$(CURDIR)/debian/emboss-doc
antiword debian/emboss-doc/usr/share/EMBOSS/doc/manuals/domainatrix.doc > debian/emboss-doc/usr/share/EMBOSS/doc/manuals/domainatrix.txt
# Remove this file when the relicenced file becomes part of the upstream tarball.
uudecode -o debian/emboss-doc/usr/share/EMBOSS/doc/manuals/EMBOSS_qg.pdf debian/EMBOSS_qg_new.pdf.uu
override_dh_auto_install-indep:
### While the next call repeats a statement from install-arch it is needed to get the
### data dir right into place. Make should be clever enough to not duplicate the process
$(MAKE) -C emboss install DESTDIR=$(EMBOSS-TMP)
ifeq ($(filter nojava,$(DEB_BUILD_PROFILES)),)
$(MAKE) -C jemboss install DESTDIR=$(CURDIR)/debian/jemboss bindir=/usr/bin
# install target seems to remove executable flag which is claimed by lintian
find debian/jemboss/usr/share/EMBOSS/jemboss/utils -type f -not -executable -name "*sh" -exec chmod a+x \{\} \;
# dangling LICEN[CS]E FILE
rm debian/jemboss/usr/share/EMBOSS/jemboss/LICENSE
# resources.jar not needed as we use the data files in /usr/share/EMBOSS/data/
rm -f debian/jemboss/usr/share/EMBOSS/jemboss/resources/resources.jar
endif
### Installation of the test suite
cp -a test debian/emboss-test/usr/share/EMBOSS/
sed -i "/SET emboss_tempdata/cSET emboss_tempdata /usr/share/EMBOSS/test" debian/emboss-test/usr/share/EMBOSS/test/.embossrc
sed -i "/SET emboss_qadata/cSET emboss_qadata /usr/share/EMBOSS/test" debian/emboss-test/usr/share/EMBOSS/test/.embossrc
mv debian/emboss-test/usr/share/EMBOSS/test/.embossrc debian/emboss-test/etc/emboss/embossrc.d/emboss-test
find debian/emboss-test/usr/share/EMBOSS/test/data -executable -type f -exec chmod a-x \{\} \;
find debian/emboss-test/usr/share/EMBOSS/test -type d -name CVS | xargs rm -rf
find debian/emboss-test/usr/share/EMBOSS/test -type f -name .cvsignore -delete
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
$(RM) test-stamp
[ -d debian/testbackup ] || cp -a test debian/testbackup
sed -i "/SET emboss_tempdata/cSET emboss_tempdata $(CURDIR)/test" test/.embossrc
sed -i "/SET emboss_qadata/cSET emboss_qadata $(CURDIR)/test" test/.embossrc
echo "SET emboss_acdroot $(CURDIR)/emboss/acd" >> test/.embossrc
echo "SET emboss_data $(CURDIR)/emboss/data" >> test/.embossrc
echo "SET emboss_docroot $(CURDIR)/doc" >> test/.embossrc
cd test/qa && LS_COLORS='' EMBOSSRC=$(CURDIR)/test PATH=$(CURDIR)/emboss:$$PATH EMBOSS_ROOT=../../../ ./qatest.csh
cat test/testdb/testdb.fasta | EMBOSS_ROOT=emboss emboss/seqret -filter
endif
override_dh_installchangelogs:
dh_installchangelogs -k ChangeLog
override_dh_installman-arch:
dh_installman -a -p emboss
for i in $(RENAMED) ; \
do dh_link usr/share/man/man1/$$i.1e.gz usr/share/man/man1/em_$$i.1e.gz ; \
done
# Target to refresh the manpages; needs libemboss-acd-perl, xsltproc, docbook-xml and docbook-xsl
manpages: debian/manpages/success
debian/manpages/success:
debian/build-manpages.sh
echo "The manpages have been sucessfully built" > debian/manpages/success
|
