03f2689f9e9e69ea8b42a8f41c8159e3bd1054e8
Merge parents 95b576d 2cf3e98
kate
  Thu Jun 30 16:24:12 2011 -0700
Merging with origin
diff --cc src/inc/sav/common.mk
index 0000000,0000000..3eb5597
new file mode 100644
--- /dev/null
+++ src/inc/sav/common.mk
@@@ -1,0 -1,0 +1,201 @@@
++CC=gcc
++# 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../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc
++
++#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 where png is installed
++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 (${PNGLIB},)
++  PNGLIB=-lpng
++endif
++
++L+=${PNGLIB}
++HG_INC+=${PNGINCL}
++
++# 32-bit color enabled by default
++ifneq (${COLOR32},0)
++    HG_DEFS+=-DCOLOR32
++endif
++
++# autodetect local installation of samtools:
++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
++
++# As we do for bam/samtools, so do for tabix.  autodetect local installation:
++ifeq (${TABIXDIR},)
++  TABIXDIR = /hive/data/outside/tabix/tabix-0.2.3/${MACHTYPE}
++  ifneq ($(wildcard ${TABIXDIR}),)
++     KNETFILE_HOOKS=1
++  endif
++endif
++ifeq (${USE_TABIX},)
++  ifneq ($(wildcard ${TABIXDIR}),)
++     USE_TABIX=1
++  endif
++endif
++
++# libtabix and Angie's KNETFILE_HOOKS extension to it: disabled by default
++ifeq (${USE_TABIX},1)
++    ifeq (${TABIXINC},)
++        TABIXINC = ${TABIXDIR}
++    endif
++    ifeq (${TABIXLIB},)
++        TABIXLIB = ${TABIXDIR}/libtabix.a
++    endif
++    HG_INC += -I${TABIXINC}
++    L+=${TABIXLIB} -lz
++    HG_DEFS+=-DUSE_TABIX
++    ifeq (${KNETFILE_HOOKS},1)
++	HG_DEFS+=-DKNETFILE_HOOKS
++    endif
++endif
++
++
++SYS = $(shell uname -s)
++
++ifeq (${HG_WARN},)
++  ifeq (${SYS},Darwin)
++      HG_WARN = -Wall -Wno-unused-variable
++      HG_WARN_UNINIT=
++  else
++    ifeq (${SYS},SunOS)
++      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 $<
++