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#!/usr/bin/make -f
# DH_VERBOSE := 1
include /usr/share/dpkg/default.mk
# Fails to build when trying to enhance hardening
export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
CMAKE_EXTRA_FLAGS += -DCONDA_BUILD=1 \
-DFETCHED_RAPMAP=1 \
-DBZIP2_LIBRARIES=-lbz2 \
-DBZIP2_INCLUDE_DIR=/usr/include \
-DLIBLZMA_INCLUDE_DIR=/usr/include/ \
-DLIBLZMA_LIBRARY=lzma \
-DLIBLZMA_HAS_AUTO_DECODER=1 \
-DLIBLZMA_HAS_EASY_ENCODER=1 \
-DLIBLZMA_HAS_LZMA_PRESET=1 \
-DCMAKE_MODULE_PATH=/usr/share/cmake/Modules \
-DTBB_WILL_RECONFIGURE=FALSE \
-DBOOST_WILL_RECONFIGURE=FALSE \
-DCMAKE_BUILD_TYPE=Release \
-DUSE_SHARED_LIBS=TRUE
%:
dh $@ --with sphinxdoc
override_dh_auto_configure:
# See here
# https://github.com/COMBINE-lab/salmon/issues/87
# for a discussion with upstream why it is necessary to include rapmap source
mkdir -p $(CURDIR)/external/install/src/rapmap
cp -av /usr/share/rapmap/src/* $(CURDIR)/external/install/src/rapmap
dh_auto_configure -- $(CMAKE_EXTRA_FLAGS)
override_dh_auto_build:
dh_auto_build
mv doc/source/license.rst doc/ # unused
PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -bhtml doc/source doc/build/html
mv doc/license.rst doc/source/
cd obj*/src && \
help2man --no-discard-stderr --no-info --name="highly-accurate, transcript-level quantification estimates from RNA-seq data"\
./salmon > ../../debian/salmon.1 && \
for option in index quant swim; do help2man --no-discard-stderr \
--version-string="$(DEB_VERSION_UPSTREAM)" --no-info "./salmon --no-version-check $${option}" \
--include=../../debian/salmon-$${option}-man-include \
> ../../debian/salmon-$${option}.1; done
override_dh_auto_install:
dh_auto_install
rm -Rvf $(CURDIR)/debian/salmon/usr/lib
# tests may fail when run out of order or concurrently
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
dh_auto_test --no-parallel
endif
override_dh_auto_clean:
dh_auto_clean
rm -rf external
rm -f debian/*.1
rm -Rf sample_data
cd doc && $(MAKE) clean
rm -rf tests/unitTests
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