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#!/usr/bin/make -f
export DH_VERBOSE = 1
export PYBUILD_NAME=bcbio
export PYBUILD_DISABLE=test # not quite ready
export PYBUILD_TEST_ARGS= -p no:cacheprovider -p no:stepwise -k 'not S3 and not rnaseq and not fusion and not srnaseq and not chipseq and not install_required and not devel and not template and not hla and not combo'
%:
dh $@ --with sphinxdoc --buildsystem=pybuild
override_dh_auto_build:
dh_auto_build
# gave error for version 1.2.3
#PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -bhtml docs build/html # HTML generator
#PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -bman docs build/man # Manpage generator
mkdir -p build/html
mkdir -p build/man && touch build/man/bcbio_nextgen.1
override_dh_auto_install:
dh_auto_install
[ -d debian/bcbio/usr/bin ] || mkdir -p debian/bcbio/usr/bin
mv debian/python3-bcbio/usr/bin/* debian/bcbio/usr/bin/
# To keep awareness of redundant binaries with different versions of Python
#mkdir -p debian/bcbio/usr/bin
#rm -rf debian/python-bcbio/usr/bin debian/python3-bcbio/usr/bin
find $(CURDIR)/debian/bcbio/usr/share/bcbio/config/ -name "*.sh" | xargs -r chmod +x
# Problem with a series of tools that need bcbio before it is installed,
# just to print --help
manpages: debian/bcbio_nextgen.1
debian/bcbio_nextgen.1: scripts/bcbio_nextgen.py
mkdir -p debian/bcbio/usr/share/man/man1
export PYTHONPATH=debian/usr/lib/python3/dist-packages ; \
for py in scripts/*.py; do \
help2man -N -s 1 --no-discard-stderr -h $$py -n $$(basename $$py .py) python | gzip -c > debian/bcbio/usr/share/man/man1/$$(basename $$py).1.gz ; \
done
# problem with --help generation
find debian -name bcbio_fastq_umi_prep.py.1* -delete
find debian -name bcbio_prepare_samples.py.1* -delete
override_dh_auto_clean:
dh_auto_clean
rm -f bcbio/pipeline/version.py
rm -f debian/*.1
rm -rf .pytest_cache
rm -f tests/data/110106_FC70BUKAAXX/1_110106_FC70BUKAAXX_1_fastq.txt
rm -f tests/data/110106_FC70BUKAAXX/1_110106_FC70BUKAAXX_2_fastq.txt
rm -f tests/data/110106_FC70BUKAAXX/2_110106_FC70BUKAAXX_1_fastq.txt
rm -f tests/data/110106_FC70BUKAAXX/2_110106_FC70BUKAAXX_2_fastq.txt
rm -f tests/data/110106_FC70BUKAAXX/3_110106_FC70BUKAAXX_fastq.txt
.PHONY: manpages
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