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#!/usr/bin/make -f
DH_VERBOSE := 1
JDIR=/usr/share/java
export CLASSPATH=${JDIR}/commons-collections4.jar:${JDIR}/gnu-getopt.jar:${JDIR}/jung-algorithms.jar:${JDIR}/jung-api.jar:${JDIR}/jung-graph-impl.jar:${JDIR}/jaligner.jar
export JAVA_HOME=/usr/lib/jvm/default-java
SOURCE_DIRECTORIES_CMAKE = Inchworm Chrysalis
SOURCE_DIRECTORIES_SIMPLE_CLEAN = trinity-plugins/slclust trinity-plugins/scaffold_iworm_contigs trinity-plugins/bamsifter
SOURCE_DIRECTORIES_SIMPLE_ALL = ${SOURCE_DIRECTORIES_SIMPLE_CLEAN} trinity-plugins/seqtk-trinity
BASEDIR=debian/trinityrnaseq/usr/lib/trinityrnaseq
EXBASEDIR=debian/trinityrnaseq-examples/usr/share/trinityrnaseq
include /usr/share/dpkg/pkg-info.mk
export BUILD_DATETIME := "$(date --utc --date="@${SOURCE_DATE_EPOCH:-$(date +%s)}" +%Y-%m-%d)"
DPKG_EXPORT_BUILDFLAGS = 1
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
include /usr/share/dpkg/buildflags.mk
%:
dh $@ --with javahelper
override_dh_autoreconf:
echo No need to run autoreconf
override_dh_auto_configure:
rm -f Chrysalis/Makefile
for target in ${SOURCE_DIRECTORIES_CMAKE}; do dh_auto_configure \
--sourcedirectory=$${target} --builddirectory=$${target}_build -- \
--prefix=/usr/lib/trinityrnaseq/$${target}; done
override_dh_auto_build:
for target in ${SOURCE_DIRECTORIES_CMAKE}; do dh_auto_build \
--sourcedirectory=$${target} --builddirectory=$${target}_build; done
for target in ${SOURCE_DIRECTORIES_SIMPLE_ALL}; do dh_auto_build \
--sourcedirectory=$${target}; done
override_dh_auto_clean:
for target in ${SOURCE_DIRECTORIES_CMAKE}; do dh_auto_clean \
--sourcedirectory=$${target} --builddirectory=$${target}_build; done
for target in ${SOURCE_DIRECTORIES_SIMPLE_CLEAN}; do dh_auto_clean \
--sourcedirectory=$${target}; done
rm --force Chrysalis/Makefile_auto
rm --force trinity-plugins/slclust/bin/slclust
cd trinity-plugins && $(MAKE) clean || true
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
java -cp Butterfly.jar TransAssembly_allProbPaths -N 10000 -L 300 \
-F 300 -C Butterfly/src/sample_data/c1.graph --stderr -V 20
endif
override_dh_auto_install:
for target in ${SOURCE_DIRECTORIES_CMAKE}; do dh_auto_install \
--sourcedirectory=$${target} --builddirectory=$${target}_build; done
for target in ${SOURCE_DIRECTORIES_SIMPLE_ALL}; do dh_auto_install \
--sourcedirectory=$${target}; done
override_dh_install-arch:
dh_install -a
find debian/trinityrnaseq -name '*.p?' | xargs sed -i \
's=^#!/usr/local/bin/perl=#!/usr/bin/perl='
chmod u+x \
${BASEDIR}/Analysis/DifferentialExpression/pairwise_summaries/class_to_separate_fpkm_matrices.pl \
${BASEDIR}/Analysis/FL_reconstruction_analysis/count_by_expression_quintile.pl \
${BASEDIR}/util/misc/capture_orig_n_unmapped_reads.pl \
${BASEDIR}/util/support_scripts/plugin_install_tests.sh \
${BASEDIR}/util/support_scripts/trinity_install_tests.sh
chmod -R a-x ${BASEDIR}/PerlLib/*.pm
chmod -R a-x ${BASEDIR}/PerlLib/*/*.pm
find debian -name __pycache__ -type d | xargs rm -rf
override_dh_install-indep:
dh_install -i
chmod u+x \
${EXBASEDIR}/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/runMe.clean.sh \
${EXBASEDIR}/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/runMe.sh \
${EXBASEDIR}/trinity_ext_sample_data/__regression_tests/test_GraphFromFasta/runMe.sh \
${EXBASEDIR}/trinity_ext_sample_data/test_Inchworm/runMe_MPI.sh \
override_dh_fixperms:
dh_fixperms
find debian -name genwig.sh -exec chmod +x \{\} \;
for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' $${pl} ; \
done
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