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Makefile.am
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Makefile.am
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# install scripts in ${bindir}
bin_SCRIPTS = \
shorah
CLEANFILES = $(bin_SCRIPTS)
EXTRA_DIST = \
.version \
meson.build \
setup.py \
src/meson.build \
src/cpp/meson.build \
src/samtools/COPYING \
src/samtools/meson.build
BUILT_SOURCES = .version
shorah: $(top_srcdir)/src/shorah/__main__.py Makefile
$(SED) 's,#!/usr/bin/env python3,#!/usr/bin/env $(PYTHON),g' $(top_srcdir)/src/shorah/__main__.py > $@
# actual C/C++ programs doing the real computation
bin_PROGRAMS = diri_sampler b2w fil
diri_sampler_SOURCES = \
src/cpp/data_structures.hpp \
src/cpp/dpm_sampler.hpp \
src/cpp/dpm_sampler.cpp
diri_sampler_CPPFLAGS = $(GSL_CFLAGS)
diri_sampler_LDADD = $(GSL_LIBS)
b2w_SOURCES = \
src/cpp/b2w.cpp
b2w_CXXFLAGS = $(PTHREAD_CFLAGS)
b2w_CPPFLAGS = -I$(top_srcdir)/src/samtools
b2w_LDADD = libbam.a $(ZLIB_LIBS) $(PTHREAD_LIBS)
fil_SOURCES = \
src/cpp/fil.cpp
fil_CXXFLAGS = $(PTHREAD_CFLAGS)
fil_CPPFLAGS = $(GSL_CFLAGS) -I$(top_srcdir)/src/samtools
fil_LDADD = libbam.a $(ZLIB_LIBS) $(GSL_LIBS) $(PTHREAD_LIBS)
noinst_LIBRARIES = libbam.a
libbam_a_SOURCES = \
src/samtools/bam.c \
src/samtools/bam.h \
src/samtools/bam_aux.c \
src/samtools/bam_cat.c \
src/samtools/bam_endian.h \
src/samtools/bam_import.c \
src/samtools/bam_index.c \
src/samtools/bam_lpileup.c \
src/samtools/bam_md.c \
src/samtools/bam_pileup.c \
src/samtools/bam_reheader.c \
src/samtools/bam_sort.c \
src/samtools/bedidx.c \
src/samtools/bgzf.c \
src/samtools/bgzf.h \
src/samtools/faidx.c \
src/samtools/faidx.h \
src/samtools/kaln.h \
src/samtools/khash.h \
src/samtools/knetfile.c \
src/samtools/knetfile.h \
src/samtools/kprobaln.c \
src/samtools/kprobaln.h \
src/samtools/kseq.h \
src/samtools/ksort.h \
src/samtools/kstring.c \
src/samtools/kstring.h \
src/samtools/razf.c \
src/samtools/razf.h \
src/samtools/sam.c \
src/samtools/sam.h \
src/samtools/sam_header.c \
src/samtools/sam_header.h
libbam_a_CPPFLAGS = $(ZLIB_CFLAGS) -D_USE_KNETFILE
libbam_a_CFLAGS = $(PTHREAD_CFLAGS)
# python modules
dist_pkgpython_PYTHON = \
src/shorah/__main__.py \
src/shorah/amplicon.py \
src/shorah/cli.py \
src/shorah/shorah_snv.py \
src/shorah/shotgun.py
pkgpython_PYTHON = .version
# example files
dist_pkgdata_DATA = \
examples/ref_genome.fasta \
examples/sample_454.fasta
ampliconpkgdatadir = $(pkgdatadir)/amplicon_test
dist_ampliconpkgdata_DATA = \
examples/amplicon_test/README.md \
examples/amplicon_test/ampli_sorted.bam \
examples/amplicon_test/amplicon_reads.fastq \
examples/amplicon_test/reference.fasta
# version handling
$(top_srcdir)/.version:
echo $(VERSION) > $@-t && mv $@-t $@
dist-hook:
echo $(VERSION) > $(distdir)/.tarball-version