| b22faf0d |
SUBDIRS = gmap gstruct
.PHONY: all clean $(SUBDIRS)
|
| 86afb162 |
OBJECTS = bamreader.o bamtally.o iit.o variantsummary.o genome.o R_init_gmapR.o
|
| b22faf0d |
R_SRC_DIR = ${CURDIR}
PREFIX = ${R_SRC_DIR}/../inst/usr
INCLUDE_DIR = $(PREFIX)/include
|
| ca5cb9d7 |
GSTRUCT_LIB = $(PREFIX)/$(LIBnn)/libgstruct-1.0.a
|
| b22faf0d |
GSTRUCT_INCLUDE_DIR = $(INCLUDE_DIR)/gstruct
SAMTOOLS_LIB = samtools/libbam.a
|
| 5bb21ad5 |
PATCH_O = samtools_patch.o
KNETFILE_O = knetfile.o
BAMOBJ_0 = \
bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o \
$(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o $(PATCH_O)
BAMOBJ=$(BAMOBJ_0:%=samtools/%)
DFLAGS = -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 \
-U_FORTIFY_SOURCE -DBGZF_CACHE \
-Dfprintf=_samtools_fprintf \
-Dexit=_samtools_exit \
-Dabort=_samtools_abort
|
| 03e8ca6d |
PKG_CPPFLAGS += -I$(INCLUDE_DIR)
|
| b22faf0d |
PKG_LIBS += $(GSTRUCT_LIB) $(SAMTOOLS_LIB) -lz
SHLIB = gmapR.so
all: $(SHLIB) gmap
$(SHLIB): $(OBJECTS) $(GSTRUCT_LIB)
$(SHLIB_LINK) -o $@ $(OBJECTS) $(ALL_LIBS)
$(OBJECTS): $(GSTRUCT_INCLUDE_DIR) $(OBJECTS:%.o=%.c)
|
| 91163a44 |
samtools/%.o: samtools/%.c
$(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) $(DFLAGS) -c $< -o $@
|
| b22faf0d |
$(GSTRUCT_LIB) $(GSTRUCT_INCLUDE_DIR): gstruct
|
| 5bb21ad5 |
$(SAMTOOLS_LIB): $(BAMOBJ)
$(AR) -crus $@ $(BAMOBJ)
|
| b22faf0d |
|
| 5bb21ad5 |
$(SUBDIRS): %: %/Makefile $(SAMTOOLS_LIB)
|
| b22faf0d |
cd $@; \
|
| 29fb70f5 |
$(MAKE) install
|
| b22faf0d |
|
| 5bb21ad5 |
gstruct/Makefile: gstruct/configure
|
| b22faf0d |
cd $(dir $@); \
|
| a49cb8de |
CFLAGS="-g -O3" \
|
| 03e8ca6d |
./configure --enable-static --disable-shared \
|
| b22faf0d |
--prefix=${PREFIX} --includedir=${GSTRUCT_INCLUDE_DIR} \
|
| 10998234 |
--libdir=${PREFIX}/${LIBnn} \
|
| 6cc263ed |
--with-samtools-lib=${R_SRC_DIR}/samtools \
|
| 15c3d797 |
--disable-maintainer-mode \
|
| 55d77a12 |
--disable-binaries
|
| b22faf0d |
## does not appear to be a true dependency yet
## --with-gmap=${PREFIX}/bin
gmap/Makefile: gmap/configure
cd $(dir $@); \
|
| c78be696 |
./configure --with-gmapdb=${GMAPDB} --prefix=${PREFIX} \
|
| ff0b3d97 |
--libdir=${PREFIX}/${LIBnn} --disable-maintainer-mode
|
| b22faf0d |
clean:
for dir in $(SUBDIRS); do \
$(MAKE) -C $$dir distclean; \
done
rm -f *.o *.so *.dll
|
