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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 = Inchworm Chrysalis trinity-plugins/*Fastool* trinity-plugins/slclust trinity-plugins/scaffold_iworm_contigs
BASEDIR=debian/trinityrnaseq/usr/lib/trinityrnaseq
EXBASEDIR=debian/trinityrnaseq-examples/usr/share/trinityrnaseq
LAST_CHANGE := $(shell dpkg-parsechangelog -S Date)
export BUILD_DATETIME := $(shell LC_ALL=C date -u -d '$(LAST_CHANGE)')
DPKG_EXPORT_BUILDFLAGS = 1
export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
include /usr/share/dpkg/buildflags.mk
%:
dh $@ --parallel --with javahelper,autoreconf
override_dh_auto_configure:
for target in ${SOURCE_DIRECTORIES}; do dh_auto_configure \
--sourcedirectory=$${target} -- \
--prefix=/usr/lib/trinityrnaseq/$${target} \
$(shell dpkg-buildflags --export=configure); done
override_dh_auto_build:
for target in ${SOURCE_DIRECTORIES}; do dh_auto_build \
-O--sourcedirectory=$${target}; done
override_dh_auto_clean:
for target in ${SOURCE_DIRECTORIES}; do dh_auto_clean \
--sourcedirectory=$${target}; done
rm --force Chrysalis/Makefile_auto
rm --force trinity-plugins/slclust/bin/slclust
override_dh_auto_test:
java -cp Butterfly.jar TransAssembly_allProbPaths -N 100 -L 100 -F 300 \
-C Butterfly/src/sample_data/RawComps.0/comp0 --stderr -V 18
override_dh_auto_install:
for target in ${SOURCE_DIRECTORIES}; do dh_auto_install \
-O--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
override_dh_install-indep:
dh_install -i
chmod u+x \
${EXBASEDIR}/sample_data/__regression_tests/test_GraphFromFasta/runMe.sh \
${EXBASEDIR}/sample_data/test_Inchworm/runMe_MPI.sh \
${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
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