Commit 1432a920 authored by zhanxw's avatar zhanxw

fix Makefile

parent daef5d27
......@@ -32,8 +32,14 @@ SAMTOOLS_LIB = $(ROOT)/third/samtools/libbam.a
RAPIDJSON_INC = $(ROOT)/third/rapidjson/include
RAPIDJSON_LIB = # We only use its headers
THIRD_INC = $(BCF_INC) $(SAMTOOLS_INC) $(TABIX_INC) $(EIGEN_INC) $(PCRE_INC) $(GSL_INC) $(ZLIB_INC) $(BZIP2_INC) $(NLOPT_INC) $(RAPIDJSON_INC)
THIRD_LIB = $(BCF_LIB) $(SAMTOOLS_LIB) $(TABIX_LIB) $(PCRE_LIB) $(GSL_LIB) $(ZLIB_LIB) $(BZIP2_LIB) $(NLOPT_LIB)
SQLITE_INC = $(ROOT)/third/sqlite/include
SQLITE_LIB = $(ROOT)/third/sqlite/lib/libsqlite3.a
ZSTD_INC = $(ROOT)/third/zstd/lib
ZSTD_LIB = $(ROOT)/third/zstd/lib/libzstd.a
THIRD_INC = $(BCF_INC) $(SAMTOOLS_INC) $(TABIX_INC) $(EIGEN_INC) $(PCRE_INC) $(GSL_INC) $(ZLIB_INC) $(BZIP2_INC) $(NLOPT_INC) $(RAPIDJSON_INC) $(SQLITE_INC) $(ZSTD_INC)
THIRD_LIB = $(BCF_LIB) $(SAMTOOLS_LIB) $(TABIX_LIB) $(PCRE_LIB) $(GSL_LIB) $(ZLIB_LIB) $(BZIP2_LIB) $(NLOPT_LIB) $(SQLITE_LIB) $(ZSTD_LIB)
##################################################
## Our libs.
BASE_INC = $(ROOT)/base
......@@ -44,6 +50,10 @@ VCF_INC = $(ROOT)/libVcf
VCF_LIB = $(ROOT)/libVcf/lib-vcf.a
VCF_LIB_DBG = $(ROOT)/libVcf/lib-dbg-vcf.a
BGEN_INC = $(ROOT)/libBgen
BGEN_LIB = $(ROOT)/libBgen/lib-bgen.a
BGEN_LIB_DBG = $(ROOT)/libBgen/lib-dbg-bgen.a
REGRESSION_INC = $(ROOT)/regression
REGRESSION_LIB = $(ROOT)/regression/lib-regression.a
REGRESSION_LIB_DBG = $(ROOT)/regression/lib-dbg-regression.a
......@@ -57,9 +67,9 @@ GONCALO_LIB_DBG = $(ROOT)/libsrc/lib-dbg-goncalo.a
CXX ?= g++
DEFAULT_CXXFLAGS = -D__STDC_LIMIT_MACROS -std=c++0x -Wall -Wno-unused-function $(OPENMP_FLAG) -DGIT_VERSION="\"$(GIT_VERSION)\""
INCLUDE = $(THIRD_INC) $(REGRESSION_INC) $(VCF_INC) $(BASE_INC) $(GONCALO_INC)
LIB = $(REGRESSION_LIB) $(VCF_LIB) $(BASE_LIB) $(GONCALO_LIB) $(THIRD_LIB)
LIB_DBG = $(REGRESSION_LIB_DBG) $(VCF_LIB_DBG) $(BASE_LIB_DBG) $(GONCALO_LIB_DBG) $(THIRD_LIB)
INCLUDE = $(THIRD_INC) $(REGRESSION_INC) $(VCF_INC) $(BGEN_INC) $(BASE_INC) $(GONCALO_INC)
LIB = $(REGRESSION_LIB) $(VCF_LIB) $(BGEN_LIB) $(BASE_LIB) $(GONCALO_LIB) $(THIRD_LIB)
LIB_DBG = $(REGRESSION_LIB_DBG) $(VCF_LIB_DBG) $(BGEN_LIB_DBG) $(BASE_LIB_DBG) $(GONCALO_LIB_DBG) $(THIRD_LIB)
CXX_INCLUDE = $(addprefix -I, $(INCLUDE)) -I. -I$(ROOT)
CXX_LIB = $(LIB) -lm -lpthread
CXX_LIB_DBG = $(LIB_DBG) -lm -lpthread
......
......@@ -30,6 +30,10 @@ $(VCF_LIB):
$(MAKE) -C $(ROOT)/libVcf $(MAKECMDGOALS)
$(VCF_LIB_DBG):
$(MAKE) -C $(ROOT)/libVcf $(MAKECMDGOALS)
$(BGEN_LIB):
$(MAKE) -C $(ROOT)/libBgen $(MAKECMDGOALS)
$(BGEN_LIB_DBG):
$(MAKE) -C $(ROOT)/libBgen $(MAKECMDGOALS)
$(REGRESSION_LIB): $(EIGEN_INC)
$(MAKE) -C $(ROOT)/regression $(MAKECMDGOALS)
$(REGRESSION_LIB_DBG):
......
......@@ -37,7 +37,7 @@ SQLITE_INC = ../third/sqlite/include
SQLITE_LIB = ../third/sqlite/lib/libsqlite3.a
ZSTD_INC = ../third/zstd/lib
ZSTD_LIB = ../thid/zstd/lib/libzstd.a
ZSTD_LIB = ../third/zstd/lib/libzstd.a
THIRD_INC = $(BCF_INC) $(TABIX_INC) $(PCRE_INC) $(BZIP2_INC) $(ZLIB_INC) $(GSL_INC) $(ZSTD_INC)
THIRD_INC_FLAGS = $(addprefix -I,$(THIRD_INC))
......
......@@ -51,7 +51,7 @@ rapidjson: rapidjson-1.0.2.tar.gz
sqlite: sqlite-autoconf-3200100.tar.gz
tar zvxf $<
-(DIR=`pwd`; cd sqlite-autoconf-3200100; ./configure --prefix="$${DIR}"/sqlite; make -j; make install)
-(DIR=`pwd`; cd sqlite-autoconf-3200100; ./configure --prefix="$${DIR}"/sqlite --enable-dynamic-extensions=no; make -j; make install)
zstd: zstd-1.3.1.tar.gz
tar zvxf $<
......
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