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head/biology/bcftools/files/patch-Makefile
| --- Makefile.orig 2015-12-15 21:42:34 UTC | --- Makefile.orig 2017-09-28 11:22:48 UTC | ||||
| +++ Makefile | +++ Makefile | ||||
| @@ -29,16 +29,15 @@ TEST_PROG= test/test-rbuf | @@ -22,10 +22,10 @@ | ||||
| all: $(PROG) $(TEST_PROG) | # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER | ||||
| # DEALINGS IN THE SOFTWARE. | |||||
| # Adjust $(HTSDIR) to point to your top-level htslib directory | |||||
| -HTSDIR = ../htslib | |||||
| -include $(HTSDIR)/htslib.mk | |||||
| -HTSLIB = $(HTSDIR)/libhts.a | |||||
| -BGZIP = $(HTSDIR)/bgzip | |||||
| -TABIX = $(HTSDIR)/tabix | |||||
| +HTSDIR = $(prefix)/include | |||||
| +HTSLIB = -lhts | |||||
| +BGZIP = $(HTSDIR)/../bin/bgzip | |||||
| +TABIX = $(HTSDIR)/../bin/tabix | |||||
| -CC = gcc | -CC = gcc | ||||
| -CPPFLAGS = | -CPPFLAGS = | ||||
| -CFLAGS = -g -Wall -Wc++-compat -O2 | -CFLAGS = -g -Wall -Wc++-compat -O2 | ||||
| -LDFLAGS = | -LDFLAGS = | ||||
| +CC ?= cc | +CC ?= cc | ||||
| +CPPFLAGS += | +CPPFLAGS += | ||||
| +CFLAGS += -Wall | +CFLAGS += -Wall | ||||
| +LDFLAGS += | +LDFLAGS += | ||||
| LIBS = | LIBS = | ||||
| OBJS = main.o vcfindex.o tabix.o \ | DYNAMIC_FLAGS = -rdynamic | ||||
| @@ -57,26 +56,20 @@ GSL_LIBS = | @@ -42,26 +42,25 @@ OBJS = main.o vcfindex.o tabix.o \ | ||||
| ifdef USE_GPL | vcfsort.o \ | ||||
| EXTRA_CPPFLAGS += -DUSE_GPL | ccall.o em.o prob1.o kmin.o # the original samtools calling | ||||
| OBJS += polysomy.o peakfit.o | |||||
| - GSL_LIBS = -lgsl -lcblas | |||||
| + GSL_LIBS = -lgsl -lgslcblas | |||||
| endif | |||||
| -prefix = /usr/local | -prefix = /usr/local | ||||
| +prefix = ${STAGEDIR}${PREFIX} | +prefix = ${PREFIX} | ||||
| exec_prefix = $(prefix) | exec_prefix = $(prefix) | ||||
| bindir = $(exec_prefix)/bin | bindir = $(exec_prefix)/bin | ||||
| libdir = $(exec_prefix)/lib | libdir = $(exec_prefix)/lib | ||||
| libexecdir = $(exec_prefix)/libexec | libexecdir = $(exec_prefix)/libexec | ||||
| -mandir = $(prefix)/share/man | -mandir = $(prefix)/share/man | ||||
| +mandir = $(prefix)/man | +mandir = $(prefix)/man | ||||
| man1dir = $(mandir)/man1 | man1dir = $(mandir)/man1 | ||||
| # Installation location for $(PLUGINS) | |||||
| plugindir = $(libexecdir)/bcftools | plugindir = $(libexecdir)/bcftools | ||||
| pluginpath = $(plugindir) | pluginpath = $(plugindir) | ||||
| # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS) | |||||
| -misc_bindir = $(bindir) | |||||
| +misc_bindir = $(bindir)/samtools_misc | |||||
| -MKDIR_P = mkdir -p | MKDIR_P = mkdir -p | ||||
| -INSTALL = install -p | -INSTALL = install -p | ||||
| -INSTALL_PROGRAM = $(INSTALL) | |||||
| -INSTALL_DATA = $(INSTALL) -m 644 | -INSTALL_DATA = $(INSTALL) -m 644 | ||||
| -INSTALL_DIR = $(MKDIR_P) -m 755 | -INSTALL_DIR = $(MKDIR_P) -m 755 | ||||
| - | -INSTALL_MAN = $(INSTALL_DATA) | ||||
| MISC_PROGRAMS = plot-vcfstats vcfutils.pl plugins/color-chrs.pl | -INSTALL_PROGRAM = $(INSTALL) | ||||
| -INSTALL_SCRIPT = $(INSTALL_PROGRAM) | |||||
| +INSTALL_DATA = ${BSD_INSTALL_DATA} | |||||
| +INSTALL_DIR = $(MKDIR_P) | |||||
| +INSTALL_MAN = ${BSD_INSTALL_MAN} | |||||
| +INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM} | |||||
| +INSTALL_SCRIPT = ${BSD_INSTALL_SCRIPT} | |||||
| all:$(PROG) plugins | PROGRAMS = bcftools | ||||
| @@ -181,7 +174,7 @@ test/test-rbuf: test/test-rbuf.o | MISC_SCRIPTS = \ | ||||
| $(CC) $(LDFLAGS) -o $@ $^ -lm $(LIBS) | @@ -77,7 +76,7 @@ all: $(PROGRAMS) $(TEST_PROGRAMS) plugin | ||||
| bcftools: $(HTSLIB) $(OBJS) | ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) | ||||
| - $(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS) | ALL_LDFLAGS = $(HTSLIB_LDFLAGS) $(LDFLAGS) | ||||
| + $(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -pthread -lz -lm $(GSL_LIBS) $(LIBS) | -ALL_LIBS = -lz -ldl $(LIBS) | ||||
| +ALL_LIBS = -lz $(LIBS) | |||||
| doc/bcftools.1: doc/bcftools.txt | # Usually config.mk and config.h are generated by running configure | ||||
| cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt | # or config.status, but if those aren't used create defaults here. | ||||
| @@ -198,8 +191,9 @@ docs: doc/bcftools.1 doc/bcftools.html | @@ -131,7 +130,7 @@ print-version: | ||||
| ifdef USE_GPL | |||||
| main.o : EXTRA_CPPFLAGS += -DUSE_GPL | |||||
| OBJS += polysomy.o peakfit.o | |||||
| - GSL_LIBS ?= -lgsl -lcblas | |||||
| + GSL_LIBS ?= -lgsl -lgslcblas | |||||
| endif | |||||
| bcftools: $(OBJS) $(HTSLIB) | |||||
| @@ -273,7 +272,7 @@ docs: doc/bcftools.1 doc/bcftools.html | |||||
| # Since there is no make dependency, bcftools.1 can be out-of-date and | # Since there is no make dependency, bcftools.1 can be out-of-date and | ||||
| # make docs can be run to update if asciidoc is available | # make docs can be run to update if asciidoc is available | ||||
| install: $(PROG) | install: $(PROG) $(PLUGINS) | ||||
| - $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir) | - $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir) | ||||
| - $(INSTALL_PROGRAM) $(PROG) $(MISC_PROGRAMS) $(DESTDIR)$(bindir) | + $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(misc_bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir) | ||||
| + $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/samtools_misc $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir) | $(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir) | ||||
| + $(INSTALL_PROGRAM) $(PROG) $(DESTDIR)$(bindir) | $(INSTALL_SCRIPT) $(MISC_SCRIPTS) $(DESTDIR)$(misc_bindir) | ||||
| + $(INSTALL_SCRIPT) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc | $(INSTALL_MAN) doc/bcftools.1 $(DESTDIR)$(man1dir) | ||||
| $(INSTALL_DATA) doc/bcftools.1 $(DESTDIR)$(man1dir) | |||||
| $(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir) | |||||