common.mk

CC=g++ -m64
#CPP=g++ -m64
# to build on sundance: CC=gcc -mcpu=v9 -m64
ifeq (${COPT},)
    COPT=-O -g
endif
CFLAGS=
HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE #-DMACHTYPE_${MACHTYPE}
#HG_INC=-I${JKSRCHOME}/inc -I${JKSRCHOME}/hg/inc -I../include

#global external libraries 
L=

# autodetect if openssl is installed
ifeq (${SSLDIR},)
  SSLDIR = /usr/include/openssl
endif
ifeq (${USE_SSL},)
  ifneq ($(wildcard ${SSLDIR}),)
     USE_SSL=1
  endif
endif


# libssl: disabled by default
ifeq (${USE_SSL},1)
    L+=-lssl -lcrypto
    HG_DEFS+=-DUSE_SSL
endif


# autodetect if png is installed
ifeq (${USE_PNG},)
  ifneq ($(wildcard /usr/include/png.h),)
    USE_PNG=1
  endif
endif

ifeq (${PNGLIB},)
  ifneq ($(wildcard /usr/lib64/libpng.a),)
      PNGLIB=/usr/lib64/libpng.a
  endif
endif
ifeq (${PNGLIB},)
  ifneq ($(wildcard /usr/lib/libpng.a),)
      PNGLIB=/usr/lib/libpng.a
  endif
endif
ifeq (${PNGLIB},)
  ifeq (${USE_PNG},1)
      PNGLIB=-lpng
  endif
endif
ifneq (${PNGLIB},)
  ifeq (${USE_PNG},)
    USE_PNG=1
  endif
endif
ifeq (${USE_PNG},)
  ifneq (${PNGLIB},)
    ifneq ($(wildcard ${PNGLIB}),)
      USE_PNG=1
    endif
  endif
endif

# libpng: disabled by default
#  for dynamic linking PNGLIB=-lpng
ifeq (${USE_PNG},1)
  L+=${PNGLIB}
  HG_DEFS+=-DUSE_PNG
  HG_INC+=${PNGINCL}

  # 32-bit color enabled by default
  ifneq (${COLOR32},0)
    HG_DEFS+=-DCOLOR32
  endif
endif

# autodetect if bam is installed
ifeq (${SAMDIR},)
  SAMDIR = /hive/data/outside/samtools/svn_${MACHTYPE}/samtools
  ifneq ($(wildcard ${SAMDIR}),)
     KNETFILE_HOOKS=1
  endif
endif
ifeq (${USE_BAM},)
  ifneq ($(wildcard ${SAMDIR}),)
     USE_BAM=1
  endif
endif

# libbam (samtools, and Angie's KNETFILE_HOOKS extension to it): disabled by default
ifeq (${USE_BAM},1)
    ifeq (${SAMINC},)
        SAMINC = ${SAMDIR}
    endif
    ifeq (${SAMLIB},)
        SAMLIB = ${SAMDIR}/libbam.a
    endif
    HG_INC += -I${SAMINC}
    L+=${SAMLIB}
    HG_DEFS+=-DUSE_BAM
    ifeq (${KNETFILE_HOOKS},1)
	HG_DEFS+=-DKNETFILE_HOOKS
    endif
endif

ifeq (${HG_WARN},)
  ifeq (darwin,$(findstring darwin,${OSTYPE}))
      HG_WARN = -Wall -Wno-unused-variable
      HG_WARN_UNINIT=
  else
    ifeq (solaris,$(findstring solaris,${OSTYPE}))
      HG_WARN = -Wall -Wformat -Wimplicit -Wreturn-type
      HG_WARN_UNINIT=-Wuninitialized
    else
      HG_WARN = -Wall -Werror #-Wformat -Wimplicit -Wreturn-type
      # HG_WARN = -Wall -Wformat -Wimplicit -Wreturn-type
      HG_WARN_UNINIT=-Wuninitialized
    endif
  endif
  # -Wuninitialized generates a warning without optimization
  ifeq ($(findstring -O,${COPT}),-O)
     HG_WARN += ${HG_WARN_UNINIT}
  endif
endif

# this is to hack around many make files not including HG_WARN in
# the link line
CFLAGS += ${HG_WARN}

ifeq (${SCRIPTS},)
    SCRIPTS=${HOME}/bin/scripts
endif
ifeq (${CGI_BIN},)
    CGI_BIN=/usr/local/apache/cgi-bin
endif
ifeq (${DOCUMENTROOT},)
    DOCUMENTROOT=/usr/local/apache/htdocs
endif
ifeq (${BINDIR},)
    BINDIR = ${HOME}/bin/${MACHTYPE}
endif
ifeq (${ENCODE_PIPELINE_BIN},)
    ENCODE_PIPELINE_BIN=/cluster/data/encode/pipeline/bin
endif

MKDIR=mkdir -p
ifeq (${STRIP},)
   STRIP=strip
endif
CVS=cvs
GIT=git

# portable naming of compiled executables: add ".exe" if compiled on 
# Windows (with cygwin).
ifeq (${OS}, Windows_NT)
  AOUT=a
  EXE=.exe
else
  AOUT=a.out
  EXE=
endif

# location of stringify program
STRINGIFY = ${DESTDIR}${BINDIR}/stringify

#Lowelab defines
#The lowelab specific code will be included in compilation if the following conditions are satistied
LOWELAB_WIKI_DEF=
LOWELAB_DEF=
ifdef LOWELAB
    LOWELAB_WIKI=1
    LOWELAB_DEF=-DLOWELAB
endif
ifdef LOWELAB_WIKI
    LOWELAB_WIKI_DEF=-DLOWELAB_WIKI
endif
LOWELAB_DEFS=${LOWELAB_DEF} ${LOWELAB_WIKI_DEF}

ifdef LOWELAB
    ifeq (${SCRIPTS},/cluster/bin/scripts)
        SCRIPTS=${HOME}/scripts
    endif
    ifeq (${CGI_BIN},/usr/local/apache/cgi-bin)
        CGI_BIN=/www/cgi-bin
    endif
    ifeq (${DOCUMENTROOT},/usr/local/apache/htdocs)
        DOCUMENTROOT=/www/browser-docs
    endif
endif

%.o: %.c
	${CC} ${COPT} ${CFLAGS} ${HG_DEFS} ${LOWELAB_DEFS} ${HG_WARN} ${HG_INC} ${XINC} -o $@ -c $<

%.o: %.cpp
	${CC} ${COPT} ${CFLAGS} ${HG_DEFS} ${LOWELAB_DEFS} ${HG_WARN} ${HG_INC} ${XINC} -o $@ -c $<


#%.o: %.cpp
#	${CPP} ${COPT} ${CFLAGS} ${HG_DEFS} ${LOWELAB_DEFS} ${HG_WARN} ${HG_INC} ${XINC} -o $@ -c $<