880d0ccc0f725d16e5b6ed9405bec57d766f0b23
markd
  Sun Dec 13 12:23:27 2020 -0800
updated snake tracks to use latest HAL, which has some perforemance improvements

diff --git src/inc/common.mk src/inc/common.mk
index c7a5997..b7eb576 100644
--- src/inc/common.mk
+++ src/inc/common.mk
@@ -56,56 +56,58 @@
 else
   ifneq ($(wildcard /opt/local/lib/libiconv.a),)
        ICONVLIB=/opt/local/lib/libiconv.a
    else
        ICONVLIB=-liconv
   endif
 endif
 
 # autodetect if openssl is installed
 ifeq (${SSLDIR},)
   SSLDIR = /usr/include/openssl
 endif
 
 # autodetect UCSC installation of hal:
 ifeq (${HALDIR},)
-    HALDIR = /hive/groups/browser/hal/halRelease/hal.2015-11-11
+    HALDIR = /hive/groups/browser/hal/build/hal.2020-12-13
     ifneq ($(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 ${HALDIR}/lib/libhdf5_hl.a -lstdc++
+    HDF5LIBS=/usr/lib64/libhdf5_cpp.a /usr/lib64/libhdf5.a /usr/lib64/libhdf5_hl.a
+    HALLIBS=${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 ${HDF5LIBS} -lcurl -lsz -lstdc++
     HG_DEFS+=-DUSE_HAL
-    HG_INC+=-I${HALDIR}/inc
+    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
 
+
 # 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${SSL_DIR}/include
 endif
 # on hgwdev, already using the static library with mysqllient.
 ifeq (${IS_HGWDEV},yes)
    L+=/hive/groups/browser/freetype/freetype-2.10.0/objs/.libs/libfreetype.a -lbz2
    L+=/usr/lib64/libssl.a /usr/lib64/libcrypto.a -lkrb5 -lk5crypto -ldl
 else
    ifneq ($(wildcard /opt/local/lib/libssl.a),)