blob: 7ae2b4c6f295ff822ce490e8a983435ad0a2fba6 (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
|
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 @@
all: $(PROG) $(TEST_PROG)
-# Adjust $(HTSDIR) to point to your top-level htslib directory
-HTSDIR = htslib-1.3.1
-include $(HTSDIR)/htslib.mk
-HTSLIB = $(HTSDIR)/libhts.a
-BGZIP = $(HTSDIR)/bgzip
-TABIX = $(HTSDIR)/tabix
+HTSDIR = /usr/include
CC = gcc
-CPPFLAGS =
-CFLAGS = -g -Wall -Wc++-compat -O2
-LDFLAGS =
-LIBS =
+CFLAGS := -g -Wall -Wc++-compat -O2 $(CFLAGS)
OBJS = main.o vcfindex.o tabix.o \
vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o \
@@ -48,7 +40,7 @@
vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o version.o \
ccall.o em.o prob1.o kmin.o # the original samtools calling
-EXTRA_CPPFLAGS = -I. -I$(HTSDIR) -DPLUGINPATH=\"$(pluginpath)\"
+EXTRA_CPPFLAGS = -I. -DPLUGINPATH=\"$(pluginpath)\"
GSL_LIBS =
# The polysomy command is not compiled by default because it brings dependency
@@ -57,7 +49,7 @@
ifdef USE_GPL
EXTRA_CPPFLAGS += -DUSE_GPL
OBJS += polysomy.o peakfit.o
- GSL_LIBS = -lgsl -lcblas
+ GSL_LIBS = -lgsl -lgslcblas
endif
prefix = /usr/local
@@ -101,11 +93,11 @@
.c.o:
$(CC) $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) -c -o $@ $<
-test: $(PROG) plugins test/test-rbuf $(BGZIP) $(TABIX)
- ./test/test.pl --exec bgzip=$(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) $(TABIX)
- ./test/test.pl --plugins --exec bgzip=$(BGZIP) --exec tabix=$(TABIX)
+test-plugins: $(PROG) plugins test/test-rbuf
+ ./test/test.pl --plugins --exec bgzip=bgzip --exec tabix=tabix
# Plugin rules
@@ -180,8 +172,8 @@
test/test-rbuf: test/test-rbuf.o
$(CC) $(LDFLAGS) -o $@ $^ -lm $(LIBS)
-bcftools: $(HTSLIB) $(OBJS)
- $(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS)
+bcftools: $(OBJS)
+ $(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) -lhts -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS)
doc/bcftools.1: doc/bcftools.txt
cd doc && a2x -adate="$(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
|