59a24235a4ba60e2f5767d05faefa89bb4ecf2db
galt
  Wed Jan 1 05:12:19 2025 -0800
fixes for common.mk to work with hgwdev and hgwdev-new. handles static compiling as much as possible.

diff --git src/inc/common.mk src/inc/common.mk
index a88196d..a49dd6a 100644
--- src/inc/common.mk
+++ src/inc/common.mk
@@ -16,35 +16,39 @@
 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 (${HOSTNAME},hgwdev-new)
+  IS_HGWDEV = yes
+else
   ifeq (${HOSTNAME},hgwdev)
     IS_HGWDEV = yes
   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
   endif
   ifneq ($(wildcard /opt/local/lib/libfreetype.a),)
     FREETYPELIBS = /opt/local/lib/libfreetype.a /opt/local/lib/libbz2.a /opt/local/lib/libbrotlidec.a /opt/local/lib/libbrotlicommon.a
   endif
@@ -154,31 +158,40 @@
     ifeq (${IS_HGWDEV},yes)
       HALDIR = /hive/groups/browser/hal/build/hal.2024-12-12
       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 ${HDF5LIBS} -lcurl -lstdc++
+    HALLIBS=${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
+    else
+      ifeq (${HOSTNAME},hgwdev)
+          HALLIBS += -lcurl /usr/lib/gcc/x86_64-redhat-linux/4.8.5/libstdc++.a
+      else
+          HALLIBS += -lcurl -lstdc++
+      endif
+    endif
     HG_DEFS+=-DUSE_HAL
     HG_INC+=-I${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
 
 ifeq (${USE_HIC},1)
     HG_DEFS+=-DUSE_HIC
 endif
@@ -255,35 +268,48 @@
     MYSQLLIBS += -lstdc++ -lrt
   endif
 endif
 
 ifeq (${ZLIB},)
   ZLIB=-lz
 endif
 
 # on hgwdev, use the static libraries
 ifeq (${IS_HGWDEV},yes)
    HG_INC += -I/cluster/software/include
    HG_INC += -I/cluster/software/include/mariadb 
    FULLWARN = yes
    L+=/hive/groups/browser/freetype/freetype-2.10.0/objs/.libs/libfreetype.a -lbz2
    L+=/cluster/software/lib64/libssl.a /cluster/software/lib64/libcrypto.a -ldl
+
+   ifeq (${HOSTNAME},hgwdev-new)
+       PNGLIB=/cluster/software/lib/libpng.a
+       PNGINCL=-I/cluster/software/include/libpng16
+   else
        PNGLIB=/usr/lib64/libpng.a
        PNGINCL=-I/usr/include/libpng15
+   endif
+
    MYSQLINC=/usr/include/mysql
    MYSQLLIBS=/cluster/software/lib64/libmariadbclient.a /cluster/software/lib64/libssl.a /cluster/software/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+=${SSLLIB}
        else
           L+=-lssl
        endif
        ifneq (${CRYPTOLIB},)
           L+=${CRYPTOLIB}
        else
           L+=-lcrypto -ldl
        endif
        ifeq (${DLLIB},)