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#!/usr/bin/make -f
#DH_VERBOSE = 1
export LC_ALL=C.UTF-8
include /usr/share/dpkg/default.mk
export PYBUILD_NAME = pbalign
BUILDDIR = $(CURDIR)/debian/python-pbalign
BINDIR=$(BUILDDIR)/usr/bin
HELP2MAN = help2man --no-info --version-string $(DEB_VERSION_UPSTREAM)
MANDIR = $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/man/man1
%:
dh $@ --with=python2 --buildsystem=pybuild
override_dh_auto_build:
dh_auto_build
$(MAKE) doc
# The tests cannot be run, mostly because the referenced data files
# (which are large) are not provided in the source distribution
#override_dh_auto_test:
# export PYTHONPATH=$(CURDIR); \
# cd tests/unit && python -m unittest discover
override_dh_install: SHELL=bash
override_dh_install:
dh_install
# Create manpages
mkdir -p $(MANDIR)
declare -A description; \
description=( \
[pbalign]="Mapping PacBio sequences to references" \
[maskAlignedReads.py]="Mask aligned reads in regions file" \
[createChemistryHeader.py]="Create a SAM header with PacBio sequencing chemistry information" \
[loadChemistry.py]="Load PacBio sequencing chemistry information" \
[extractUnmappedSubreads.py]="Extract unmapped subreads from a fasta file" \
); \
export PYTHONPATH=$(BUILDDIR)/usr/lib/python2.7/dist-packages; \
for executable in $(BUILDDIR)/usr/bin/*; \
do \
$(HELP2MAN) --name="$${description[`basename $$executable`]}" \
$$executable > $(MANDIR)/`basename $$executable.1`; \
done
# Remove .py suffix from scripts (we'll make symlinks to replace them)
for script in extractUnmappedSubreads \
loadChemistry \
createChemistryHeader \
maskAlignedReads; \
do \
mv $(BINDIR)/$$script.py $(BINDIR)/$$script; \
mv $(MANDIR)/$$script.py.1 $(MANDIR)/$$script.1; \
done
# Place executables in the pbalign package
mkdir -p $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin
mv $(BINDIR)/* $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin
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