1f0f06ed4995b90bd4336fc87cb8beda20ca39b7
galt
  Fri Jan 10 18:20:48 2025 -0800
fix for hgwdev-new to use /cluster/software/r9 for specially compiled R9 libs instead of /culster/sofware which has been correctly recompield for R7 libs. So now both hggwdev and hgwdev-new are correct and not mixed up for compiling.

diff --git src/inc/common.mk src/inc/common.mk
index ed07a2d..02685b9 100644
--- src/inc/common.mk
+++ src/inc/common.mk
@@ -18,33 +18,35 @@
 #    $(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 (${HOSTNAME},hgwdev-new)
   IS_HGWDEV = yes
+  OURSTUFF = /cluster/software/r9
 else
   ifeq (${HOSTNAME},hgwdev)
     IS_HGWDEV = yes
+    OURSTUFF = /cluster/software
   else
      IS_HGWDEV = no
   endif
 endif
 
 # for Darwin (Mac OSX), use static libs when they can be found
 ifeq ($(UNAME_S),Darwin)
   ifneq ($(wildcard /opt/local/include/openssl/ssl.h),)
     HG_INC += -I/opt/local/include
   endif
   ifneq ($(wildcard /opt/local/lib/libz.a),)
     ZLIB = /opt/local/lib/libz.a
   endif
   ifneq ($(wildcard /opt/local/lib/libpng.a),)
     PNGLIB = /opt/local/lib/libpng.a
@@ -161,34 +163,34 @@
       ifneq ($(wildcard ${HALDIR}),)
         ifeq (${USE_HAL},)
           USE_HAL=1
         endif
       endif
     endif
 endif
 
 ifeq (${USE_HAL},1)
     # force static libraries to keep programs portable
     HDF5DIR=/hive/groups/browser/hal/build/hdf5-1.12.0
     HDF5LIBDIR=${HDF5DIR}/local/lib
     HDF5LIBS=${HDF5LIBDIR}/libhdf5_cpp.a ${HDF5LIBDIR}/libhdf5.a ${HDF5LIBDIR}/libhdf5_hl.a
     HALLIBS=${HALDIR}/hal/lib/libHalBlockViz.a ${HALDIR}/hal/lib/libHalMaf.a ${HALDIR}/hal/lib/libHalLiftover.a ${HALDIR}/hal/lib/libHalLod.a ${HALDIR}/hal/lib/libHal.a ${HALDIR}/sonLib/lib/sonLib.a ${HDF5LIBS} -lz
     ifeq (${HOSTNAME},hgwdev-new)
-        HALLIBS += /cluster/software/lib/libcurl.a /usr/lib/gcc/x86_64-redhat-linux/11/libstdc++.a
+        HALLIBS += ${OURSTUFF}/lib/libcurl.a /usr/lib/gcc/x86_64-redhat-linux/11/libstdc++.a
     else
       ifeq (${HOSTNAME},hgwdev)
-          HALLIBS += /cluster/software/lib/libcurl.a /usr/lib/gcc/x86_64-redhat-linux/4.8.5/libstdc++.a
+          HALLIBS += ${OURSTUFF}/lib/libcurl.a /usr/lib/gcc/x86_64-redhat-linux/4.8.5/libstdc++.a
       else
           HALLIBS += -lcurl -lstdc++
       endif
     endif
     HG_DEFS+=-DUSE_HAL
     HG_INC+=-I${HALDIR}/inc -I${HALDIR}/hal/blockViz/inc
 endif
 # on hgwdev, include HAL by defaults
 ifeq (${IS_HGWDEV},yes)
    L+=${HALLIBS}
 endif
 
 ifeq (${USE_HIC},)
     USE_HIC=1
 endif
@@ -264,48 +266,48 @@
 #    MySQL version 5.6 libraries, but no 'librt' on Mac OSX
 ifeq (${IS_HGWDEV},no)
   ifeq ($(UNAME_S),Darwin)
     MYSQLLIBS += -lstdc++
   else
     MYSQLLIBS += -lstdc++ -lrt
   endif
 endif
 
 ifeq (${ZLIB},)
   ZLIB=-lz
 endif
 
 # on hgwdev, use the static libraries
 ifeq (${IS_HGWDEV},yes)
-   HG_INC += -I/cluster/software/include
-   HG_INC += -I/cluster/software/include/mariadb 
+   HG_INC += -I${OURSTUFF}/include
+   HG_INC += -I${OURSTUFF}/include/mariadb 
    FULLWARN = yes
    L+=/hive/groups/browser/freetype/freetype-2.10.0/objs/.libs/libfreetype.a
-   L+=/cluster/software/lib64/libssl.a /cluster/software/lib64/libcrypto.a -ldl
+   L+=${OURSTUFF}/lib64/libssl.a ${OURSTUFF}/lib64/libcrypto.a -ldl
 
    ifeq (${HOSTNAME},hgwdev-new)
-       PNGLIB=/cluster/software/lib/libpng.a
-       PNGINCL=-I/cluster/software/include/libpng16
+       PNGLIB=${OURSTUFF}/lib/libpng.a
+       PNGINCL=-I${OURSTUFF}/include/libpng16
        L += /lib64/libbz2.a
    else
        PNGLIB=/usr/lib64/libpng.a
        PNGINCL=-I/usr/include/libpng15
        L += -lbz2
    endif
 
    MYSQLINC=/usr/include/mysql
-   MYSQLLIBS=/cluster/software/lib64/libmariadbclient.a /cluster/software/lib64/libssl.a /cluster/software/lib64/libcrypto.a -ldl -lz
+   MYSQLLIBS=${OURSTUFF}/lib64/libmariadbclient.a ${OURSTUFF}/lib64/libssl.a ${OURSTUFF}/lib64/libcrypto.a -ldl -lz
 
    ifeq (${HOSTNAME},hgwdev-new)
        MYSQLLIBS += /usr/lib/gcc/x86_64-redhat-linux/11/libstdc++.a /usr/lib64/librt.a
    else
        MYSQLLIBS += /usr/lib/gcc/x86_64-redhat-linux/4.8.5/libstdc++.a /usr/lib64/librt.a
    endif
 
 else
    ifeq (${CONDA_BUILD},1)
        L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl
    else
        ifneq (${SSLLIB},)
           L+=${SSLLIB}
        else
           L+=-lssl