a4c0a9f4b48c074daec96559640b76ab2d9db488
galt
  Mon Aug 13 16:03:28 2018 -0700
experiment finished.

diff --git src/inc/common.mk.galt src/inc/common.mk.galt
deleted file mode 100644
index d2e6e4c..0000000
--- src/inc/common.mk.galt
+++ /dev/null
@@ -1,428 +0,0 @@
-# if CC is undefined, set it to gcc
-CC?=gcc
-# to build on sundance: CC=gcc -mcpu=v9 -m64
-ifeq (${COPT},)
-    COPT=-O -g
-endif
-ifeq (${CFLAGS},)
-    CFLAGS=
-endif
-ifeq (${MACHTYPE},)
-    MACHTYPE:=$(shell uname -m)
-#    $(info MACHTYPE was empty, set to: ${MACHTYPE})
-endif
-ifneq (,$(findstring -,$(MACHTYPE)))
-#    $(info MACHTYPE has - sign ${MACHTYPE})
-    MACHTYPE:=$(shell uname -m)
-#    $(info MACHTYPE has - sign set to: ${MACHTYPE})
-endif
-
-HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE}
-HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib
-
-# to check for Mac OSX Darwin specifics:
-UNAME_S := $(shell uname -s)
-# to check for builds on hgwdev
-HOSTNAME = $(shell uname -n)
-
-ifeq (${HOSTNAME},hgwdev)
-  IS_HGWDEV = yes
-else
-  IS_HGWDEV = no
-endif
-
-ifeq (${IS_HGWDEV},yes)
-  FULLWARN = yes
-endif
-
-ifeq (${HOSTNAME},cirm-01)
-  FULLWARN = yes
-endif
-
-ifeq (${PTHREADLIB},)
-  PTHREADLIB=-lpthread
-endif
-
-# pthreads is required
-ifneq ($(UNAME_S),Darwin)
-  L+=${PTHREADLIB}
-endif
-
-# autodetect if openssl is installed
-ifeq (${SSLDIR},)
-  SSLDIR = /usr/include/openssl
-endif
-
-# autodetect UCSC installation of hal:
-ifeq (${HALDIR},)
-    HALDIR = /hive/groups/browser/hal/halRelease
-    ifneq ($(wildcard ${HALDIR}),)
-        ifeq (${USE_HAL},)
-          USE_HAL=1
-        endif
-    endif
-endif
-
-ifeq (${USE_HAL},1)
-    HALLIBS=${HALDIR}/lib/halMaf.a ${HALDIR}/lib/halChain.a ${HALDIR}/lib/halMaf.a ${HALDIR}/lib/halLiftover.a ${HALDIR}/lib/halLod.a ${HALDIR}/lib/halLib.a ${HALDIR}/lib/sonLib.a ${HALDIR}/lib/libhdf5_cpp.a ${HALDIR}/lib/libhdf5.a ${HALDIR}/lib/libhdf5_hl.a
-    HG_DEFS+=-DUSE_HAL
-    HG_INC+=-I${HALDIR}/inc
-endif
-
-
-# libssl: disabled by default
-ifneq (${SSL_DIR}, "/usr/include/openssl")
-  ifneq ($(UNAME_S),Darwin)
-    ifneq ($(wildcard ${SSL_DIR}),)
-      L+=-L${SSL_DIR}/lib
-    endif
-  endif
-    HG_INC+=-I${SSL_DIR}/include
-endif
-# on hgwdev, already using the static library with mysqlclient.
-ifeq (${IS_HGWDEV},yes)
-   L+=/usr/lib64/libssl.a /usr/lib64/libcrypto.a -lkrb5 -lk5crypto
-   # at the moment, this is mostly redundant. but that could be fixed
-   #GALT L+=/usr/lib64/libssl.a /usr/lib64/libcrypto.a -lkrb5
-else
-   L+=-lssl -lcrypto
-endif
-
-# autodetect where libm is installed
-ifeq (${MLIB},)
-  ifneq ($(wildcard /usr/lib64/libm.a),)
-      MLIB=
-      #GALT MLIB=/usr/lib64/libm.a
-  endif
-endif
-ifeq (${MLIB},)
-  MLIB=-lm
-endif
-
-# autodetect where png is installed
-ifeq (${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},)
-  ifneq ($(wildcard /opt/local/lib/libpng.a),)
-      PNGLIB=/opt/local/lib/libpng.a
-  endif
-endif
-ifeq (${PNGLIB},)
-  ifneq ($(wildcard /usr/local/lib/libpng.a),)
-      PNGLIB=/usr/local/lib/libpng.a
-  endif
-endif
-ifeq (${PNGLIB},)
-      PNGLIB := $(shell libpng-config --ldflags  || true)
-endif
-ifeq (${PNGLIB},)
-  PNGLIB=-lpng
-endif
-ifeq (${PNGINCL},)
-  ifneq ($(wildcard /opt/local/include/png.h),)
-      PNGINCL=-I/opt/local/include
-  else
-      PNGINCL := $(shell libpng-config --I_opts  || true)
-#       $(info using libpng-config to set PNGINCL: ${PNGINCL})
-  endif
-endif
-
-# autodetect where mysql includes and libraries are installed
-# do not need to do this during 'clean' target (this is very slow for 'clean')
-ifneq ($(MAKECMDGOALS),clean)
-  # on hgwdev, use the static library.
-  ifeq (${IS_HGWDEV},yes)
-    MYSQLINC=/usr/include/mysql
-    #MYSQLLIBS=/usr/lib64/libmysqlclient.a
-    MYSQLLIBS=/usr/lib64/libmysqlclient.a /usr/lib64/libssl.a /usr/lib64/libcrypto.a -lkrb5 -lk5crypto -ldl
-    #GALT MYSQLLIBS=/usr/lib64/libssl.a /usr/lib64/libcrypto.a /usr/lib64/mysql/libmysqlclient.a -lkrb5
-  endif
-  # this does *not* work on Mac OSX with the dynamic libraries
-  ifneq ($(UNAME_S),Darwin)
-    ifeq (${MYSQLLIBS},)
-      MYSQLLIBS := $(shell mysql_config --libs || true)
-#        $(info using mysql_config to set MYSQLLIBS: ${MYSQLLIBS})
-    endif
-  endif
-
-  ifeq (${MYSQLINC},)
-    MYSQLINC := $(shell mysql_config --include | sed -e 's/-I//' || true)
-#        $(info using mysql_config to set MYSQLINC: ${MYSQLINC})
-  endif
-  ifeq (${MYSQLINC},)
-    ifneq ($(wildcard /usr/local/mysql/include/mysql.h),)
-	  MYSQLINC=/usr/local/mysql/include
-    endif
-  endif
-  ifeq (${MYSQLINC},)
-    ifneq ($(wildcard /usr/include/mysql/mysql.h),)
-	  MYSQLINC=/usr/include/mysql
-    endif
-  endif
-  ifeq (${MYSQLINC},)
-    ifneq ($(wildcard /opt/local/include/mysql57/mysql/mysql.h),)
-	  MYSQLINC=/opt/local/include/mysql57/mysql
-    endif
-  endif
-  ifeq (${MYSQLINC},)
-    ifneq ($(wildcard /opt/local/include/mysql55/mysql/mysql.h),)
-	  MYSQLINC=/opt/local/include/mysql55/mysql
-    endif
-  endif
-  ifeq (${MYSQLLIBS},)
-    ifneq ($(wildcard /opt/local/lib/mysql57/mysql/libmysqlclient.a),)
-	  MYSQLLIBS=/opt/local/lib/mysql57/mysql/libmysqlclient.a
-    endif
-  endif
-  ifeq (${MYSQLLIBS},)
-    ifneq ($(wildcard /opt/local/lib/mysql55/mysql/libmysqlclient.a),)
-	  MYSQLLIBS=/opt/local/lib/mysql55/mysql/libmysqlclient.a
-    endif
-  endif
-  ifeq (${MYSQLLIBS},)
-    ifneq ($(wildcard /usr/lib64/mysql/libmysqlclient.a),)
-	  MYSQLLIBS=/usr/lib64/mysql/libmysqlclient.a
-    endif
-  endif
-  ifeq (${MYSQLLIBS},)
-    ifneq ($(wildcard /usr/local/mysql/lib/libmysqlclient.a),)
-	  MYSQLLIBS=/usr/local/mysql/lib/libmysqlclient.a
-    endif
-  endif
-  ifeq (${MYSQLLIBS},)
-    ifneq ($(wildcard /usr/local/mysql/lib/libmysqlclient.a),)
-	  MYSQLLIBS=/usr/local/mysql/lib/libmysqlclient.a
-    endif
-  endif
-  ifeq (${MYSQLLIBS},)
-    ifneq ($(wildcard /usr/lib64/mysql/libmysqlclient.so),)
-	  MYSQLLIBS=/usr/lib64/mysql/libmysqlclient.so
-    endif
-  endif
-  ifeq (${MYSQLLIBS},)
-    ifneq ($(wildcard /usr/lib/libmysqlclient.a),)
-	  MYSQLLIBS=/usr/lib/libmysqlclient.a
-    endif
-  endif
-  ifeq (${MYSQLLIBS},)
-    ifneq ($(wildcard /opt/local/lib/mysql55/mysql/libmysqlclient.a),)
-	  MYSQLLIBS=/opt/local/lib/mysql55/mysql/libmysqlclient.a
-    endif
-  endif
-  ifeq (${MYSQLLIBS},)
-    ifneq ($(wildcard /usr/local/Cellar/mysql/5.6.19/lib/libmysqlclient.a),)
-	  MYSQLLIBS=/usr/local/Cellar/mysql/5.6.19/lib/libmysqlclient.a
-    endif
-  endif
-  ifeq (${MYSQLLIBS},)
-    ifneq ($(wildcard /usr/local/Cellar/mysql/5.6.16/lib/libmysqlclient.a),)
-	  MYSQLLIBS=/usr/local/Cellar/mysql/5.6.16/lib/libmysqlclient.a
-    endif
-  endif
-  ifeq ($(findstring src/hg/,${CURDIR}),src/hg/)
-    ifeq (${MYSQLINC},)
-        $(error can not find installed mysql development system)
-    endif
-  endif
-    # last resort, hoping the compiler can find it in standard locations
-  ifeq (${MYSQLLIBS},)
-      MYSQLLIBS="-lmysqlclient"
-  endif
-endif
-
-# $(info have MYSQLINC: ${MYSQLINC})
-# $(info have MYSQLLIBS: ${MYSQLLIBS})
-
-# OK to add -lstdc++ to all MYSQLLIBS just in case it is
-#    MySQL version 5.6 libraries, but no 'librt' on Mac OSX
-ifeq (${IS_HGWDEV},yes)
-  MYSQLLIBS += /usr/lib/gcc/x86_64-redhat-linux/4.8.2/libstdc++.a /usr/lib/x86_64-redhat-linux6E/lib64/librt.a
-  #GALT MYSQLLIBS += /usr/lib/gcc/x86_64-redhat-linux/4.4.4/libstdc++.a /usr/lib/debug/usr/lib64/librt.a
-else
-  ifeq ($(UNAME_S),Darwin)
-    MYSQLLIBS += -lstdc++
-  else
-    MYSQLLIBS += -lstdc++ -lrt
-  endif
-endif
-
-ifeq (${ZLIB},)
-  ZLIB=-lz
-  ifneq ($(wildcard /opt/local/lib/libz.a),)
-    ZLIB=/opt/local/lib/libz.a
-  endif
-  ifneq ($(wildcard /usr/lib64/libz.a),)
-    ZLIB=/usr/lib64/libz.a
-  endif
-endif
-
-#global external libraries
-L += $(kentSrc)/htslib/libhts.a
-
-L+=${PNGLIB} ${ZLIB} ${MLIB}
-HG_INC+=${PNGINCL}
-
-# pass through COREDUMP
-ifneq (${COREDUMP},)
-    HG_DEFS+=-DCOREDUMP
-endif
-
-# autodetect UCSC additional source code with password for some external tracks on gbib
-GBIBDIR = /hive/groups/browser/gbib/
-ifneq ($(wildcard ${GBIBDIR}/*.c),)
-  HG_DEFS+=-DUSE_GBIB_PWD
-  HG_INC += -I${GBIBDIR}
-endif
-
-SYS = $(shell uname -s)
-
-ifeq (${HG_WARN},)
-  ifeq (${SYS},Darwin)
-      HG_WARN = -Wall -Wno-unused-variable -Wno-deprecated-declarations
-      HG_WARN_UNINIT=
-  else
-    ifeq (${SYS},SunOS)
-      HG_WARN = -Wall -Wformat -Wimplicit -Wreturn-type
-      HG_WARN_UNINIT=-Wuninitialized
-    else
-      ifeq (${FULLWARN},yes)
-        HG_WARN = -Wall -Werror -Wformat -Wformat-security -Wimplicit -Wreturn-type -Wempty-body -Wunused-but-set-variable
-        HG_WARN_UNINIT=-Wuninitialized
-      else
-        HG_WARN = -Wall -Wformat -Wimplicit -Wreturn-type
-        HG_WARN_UNINIT=-Wuninitialized
-      endif
-    endif
-  endif
-  # -Wuninitialized generates a warning without optimization
-  ifeq ($(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 (${ENCODE_PIPELINE_BIN},)
-    ENCODE_PIPELINE_BIN=/cluster/data/encode/pipeline/bin
-endif
-
-# avoid an extra leading slash when DESTDIR is empty
-ifeq (${DESTDIR},)
-  DESTBINDIR=${BINDIR}
-else
-  DESTBINDIR=${DESTDIR}/${BINDIR}
-endif
-
-# location of stringify program
-STRINGIFY = ${DESTBINDIR}/stringify
-
-MKDIR=mkdir -p
-ifeq (${STRIP},)
-   STRIP=true
-endif
-CVS=cvs
-GIT=git
-
-# portable naming of compiled executables: add ".exe" if compiled on
-# Windows (with cygwin).
-ifeq (${OS}, Windows_NT)
-  AOUT=a
-  EXE=.exe
-else
-  AOUT=a.out
-  EXE=
-endif
-
-#Lowelab defines
-#The lowelab specific code will be included in compilation if the following conditions are satistied
-LOWELAB_WIKI_DEF=
-LOWELAB_DEF=
-ifdef LOWELAB
-    LOWELAB_WIKI=1
-    LOWELAB_DEF=-DLOWELAB
-endif
-ifdef LOWELAB_WIKI
-    LOWELAB_WIKI_DEF=-DLOWELAB_WIKI
-endif
-LOWELAB_DEFS=${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 $<
-
-# autodetect UCSC installation of node.js:
-ifeq (${NODEBIN},)
-    NODEBIN = /cluster/software/src/node-v0.10.24-linux-x64/bin
-    ifeq ($(wildcard ${NODEBIN}),)
-	NODEBIN=
-    endif
-endif
-
-# node.js tools: jshint, jsx, jsxhint, uglifyjs, ...
-ifeq (${JSHINT},)
-    JSHINT=${NODEBIN}/jshint
-    ifeq ($(wildcard ${JSHINT}),)
-	    JSHINT=true
-    endif
-endif
-ifeq (${JSXHINT},)
-    JSXHINT=${NODEBIN}/jsxhint
-    ifeq ($(wildcard ${JSXHINT}),)
-        JSXHINT=true
-    endif
-endif
-ifeq (${JSX},)
-    JSX=${NODEBIN}/jsx
-    ifeq ($(wildcard ${JSX}),)
-        JSX=true
-    endif
-endif
-ifeq (${UGLIFYJS},)
-    UGLIFYJS=${NODEBIN}/uglifyjs
-    ifeq ($(wildcard ${UGLIFYJS}),)
-        UGLIFYJS=true
-    endif
-endif