02a57750d003fe08e6075b904e0fc8e3abf90b99
kate
  Wed Jan 9 11:40:36 2013 -0800
Make common.mk consistent with policy of not stripping binaries by default (Mark D. recommendation, on advisement from Hiram). This takes care of all those directories that haven't had strip removed or commented out of makefiles (e.g. tools)
diff --git src/inc/common.mk src/inc/common.mk
index 05e3880..3942ec9 100644
--- src/inc/common.mk
+++ src/inc/common.mk
@@ -1,222 +1,222 @@
 CC=gcc
 # to build on sundance: CC=gcc -mcpu=v9 -m64
 ifeq (${COPT},)
     COPT=-O -g
 endif
 ifeq (${CFLAGS},)
     CFLAGS=
 endif
 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=
 
 # pthreads is required
 L+=-pthread
 
 # 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 UCSC installation of samtabix:
 ifeq (${SAMTABIXDIR},)
     SAMTABIXDIR = /hive/data/outside/samtabix/${MACHTYPE}
     ifneq ($(wildcard ${SAMTABIXDIR}),)
         ifeq (${USE_SAMTABIX},)
           USE_SAMTABIX=1
         endif
     endif
 endif
 
 # libsamtabix (samtools + tabix + Angie's KNETFILE_HOOKS extension to it): disabled by default
 ifeq (${USE_SAMTABIX},1)
     KNETFILE_HOOKS=1
     USE_BAM=1
     USE_TABIX=1
     ifeq (${SAMTABIXINC},)
         SAMTABIXINC = ${SAMTABIXDIR}
     endif
     ifeq (${SAMTABIXLIB},)
         SAMTABIXLIB = ${SAMTABIXDIR}/libsamtabix.a
     endif
     HG_INC += -I${SAMTABIXINC}
     L+=${SAMTABIXLIB} -lz
     HG_DEFS+=-DUSE_SAMTABIX -DUSE_BAM -DUSE_TABIX -DKNETFILE_HOOKS
 else
   # Deprecated but supported for mirrors, for now: independent samtools and tabix libs
 
   # 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
 
   # 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
 endif
 
 SYS = $(shell uname -s)
 FULLWARN = $(shell uname -n)
 
 ifeq (${HG_WARN},)
   ifeq (${SYS},Darwin)
       HG_WARN = -Wall -Wno-unused-variable
       HG_WARN_UNINIT=
   else
     ifeq (${SYS},SunOS)
       HG_WARN = -Wall -Wformat -Wimplicit -Wreturn-type
       HG_WARN_UNINIT=-Wuninitialized
     else
       ifeq (${FULLWARN},hgwdev)
         HG_WARN = -Wall -Werror -Wformat -Wimplicit -Wreturn-type
         HG_WARN_UNINIT=-Wuninitialized
       else
         HG_WARN = -Wall -Wformat -Wimplicit -Wreturn-type
         HG_WARN_UNINIT=-Wuninitialized
       endif
     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
+   STRIP=echo
 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
 
 #ENCODE COMMON VARIABLES
 CONFIG_FILES = \
 	fields.ra \
 	labs.ra
 CV = cv.ra
 CVDIR=${HOME}/kent/src/hg/makeDb/trackDb/cv/alpha
 PIPELINE_PATH=/hive/groups/encode/dcc/pipeline
 CONFIG_DIR = ${PIPELINE_PATH}/${PIPELINE_DIR}/config
 ENCODEDCC_DIR = ${PIPELINE_PATH}/downloads/encodeDCC
 
 %.o: %.c
 	${CC} ${COPT} ${CFLAGS} ${HG_DEFS} ${LOWELAB_DEFS} ${HG_WARN} ${HG_INC} ${XINC} -o $@ -c $<