diff options
Diffstat (limited to 'makefile-system-htslib.patch')
| -rw-r--r-- | makefile-system-htslib.patch | 60 |
1 files changed, 38 insertions, 22 deletions
diff --git a/makefile-system-htslib.patch b/makefile-system-htslib.patch index 7ae2b4c6f295..5cebf3c5d3b8 100644 --- a/makefile-system-htslib.patch +++ b/makefile-system-htslib.patch @@ -1,16 +1,17 @@ -diff -aur /tmp/makepkg/bcftools/src/bcftools-1.3.1/Makefile /tmp/makepkg/bcftools/src/bcftools-1.3.1-patched/Makefile ---- /tmp/makepkg/bcftools/src/bcftools-1.3.1/Makefile 2016-04-22 11:50:59.000000000 +0200 -+++ /tmp/makepkg/bcftools/src/bcftools-1.3.1-patched/Makefile 2016-05-29 20:18:22.323268586 +0200 -@@ -28,18 +28,10 @@ - +--- Makefile.orig 2017-03-14 07:26:49.191430557 +0100 ++++ Makefile 2017-03-14 07:27:44.929678345 +0100 +@@ -29,20 +29,10 @@ all: $(PROG) $(TEST_PROG) --# Adjust $(HTSDIR) to point to your top-level htslib directory --HTSDIR = htslib-1.3.1 + # Adjust $(HTSDIR) to point to your top-level htslib directory +-HTSDIR = htslib-1.4 -include $(HTSDIR)/htslib.mk +-include $(HTSDIR)/htslib_static.mk -HTSLIB = $(HTSDIR)/libhts.a -BGZIP = $(HTSDIR)/bgzip -TABIX = $(HTSDIR)/tabix +-HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS) +-HTSLIB_LIBS = $(HTSLIB_static_LIBS) +HTSDIR = /usr/include CC = gcc @@ -20,10 +21,21 @@ diff -aur /tmp/makepkg/bcftools/src/bcftools-1.3.1/Makefile /tmp/makepkg/bcftool -LIBS = +CFLAGS := -g -Wall -Wc++-compat -O2 $(CFLAGS) + ifeq "$(shell uname -s)" "Darwin" + DYNAMIC_FLAGS = -Wl,-export_dynamic +@@ -51,8 +41,8 @@ + endif + + # TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally +-ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) +-ALL_LDFLAGS = $(DYNAMIC_FLAGS) $(HTSLIB_LDFLAGS) $(LDFLAGS) ++ALL_CPPFLAGS = -I. $(CPPFLAGS) ++ALL_LDFLAGS = $(DYNAMIC_FLAGS) $(LDFLAGS) + ALL_LIBS = -lm -lz -ldl $(LIBS) + OBJS = main.o vcfindex.o tabix.o \ - vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o \ -@@ -48,7 +40,7 @@ - vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o version.o \ +@@ -64,7 +54,7 @@ + mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o \ ccall.o em.o prob1.o kmin.o # the original samtools calling -EXTRA_CPPFLAGS = -I. -I$(HTSDIR) -DPLUGINPATH=\"$(pluginpath)\" @@ -31,7 +43,7 @@ diff -aur /tmp/makepkg/bcftools/src/bcftools-1.3.1/Makefile /tmp/makepkg/bcftool GSL_LIBS = # The polysomy command is not compiled by default because it brings dependency -@@ -57,7 +49,7 @@ +@@ -73,7 +63,7 @@ ifdef USE_GPL EXTRA_CPPFLAGS += -DUSE_GPL OBJS += polysomy.o peakfit.o @@ -40,13 +52,14 @@ diff -aur /tmp/makepkg/bcftools/src/bcftools-1.3.1/Makefile /tmp/makepkg/bcftool endif prefix = /usr/local -@@ -101,11 +93,11 @@ +@@ -117,12 +107,12 @@ .c.o: - $(CC) $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) -c -o $@ $< + $(CC) $(CFLAGS) $(EXTRA_CPPFLAGS) $(ALL_CPPFLAGS) -c -o $@ $< --test: $(PROG) plugins test/test-rbuf $(BGZIP) $(TABIX) +-test: $(PROG) plugins test/test-rbuf test/test-regidx $(BGZIP) $(TABIX) ++test: $(PROG) plugins test/test-rbuf test/test-regidx + ./test/test-regidx - ./test/test.pl --exec bgzip=$(BGZIP) --exec tabix=$(TABIX) -+test: $(PROG) plugins test/test-rbuf + ./test/test.pl --exec bgzip=bgzip --exec tabix=tabix -test-plugins: $(PROG) plugins test/test-rbuf $(BGZIP) $(TABIX) @@ -56,16 +69,19 @@ diff -aur /tmp/makepkg/bcftools/src/bcftools-1.3.1/Makefile /tmp/makepkg/bcftool # Plugin rules -@@ -180,8 +172,8 @@ - test/test-rbuf: test/test-rbuf.o - $(CC) $(LDFLAGS) -o $@ $^ -lm $(LIBS) +@@ -208,11 +198,11 @@ + + test/test-regidx.o: test/test-regidx.c regidx.h + +-test/test-regidx: test/test-regidx.o regidx.o $(HTSLIB) +- $(CC) $(ALL_LDFLAGS) -o $@ $^ $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(ALL_LIBS) ++test/test-regidx: test/test-regidx.o regidx.o ++ $(CC) $(ALL_LDFLAGS) -o $@ $^ -lpthread -lhts $(ALL_LIBS) -bcftools: $(HTSLIB) $(OBJS) -- $(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS) +- $(CC) $(ALL_LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(GSL_LIBS) $(ALL_LIBS) +bcftools: $(OBJS) -+ $(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) -lhts -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS) ++ $(CC) $(ALL_LDFLAGS) -o $@ $(OBJS) -lpthread -lhts $(GSL_LIBS) $(ALL_LIBS) doc/bcftools.1: doc/bcftools.txt cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt -Only in /tmp/makepkg/bcftools/src/bcftools-1.3.1-patched: Makefile.orig -Only in /tmp/makepkg/bcftools/src/bcftools-1.3.1-patched: Makefile.rej |