b763a93bef738004614cb657ccab6805f94dda8e
braney
  Thu Aug 15 19:06:39 2013 -0700
make HAL linked in by default, fix the problem with mismatched bases nothaving the right chars in them, start adding HAL to the table browser.
refs #10637

diff --git src/inc/common.mk src/inc/common.mk
index 7f9322f..a4eefc8 100644
--- src/inc/common.mk
+++ src/inc/common.mk
@@ -14,37 +14,47 @@
 
 # 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
 
 
-# libhal: disabled by default
+# autodetect UCSC installation of hal:
+ifeq (${HALDIR},)
+    HALDIR = /hive/groups/browser/hal
+    ifneq ($(wildcard ${HALDIR}),)
+        ifeq (${USE_HAL},)
+          USE_HAL=1
+        endif
+    endif
+endif
+
 ifeq (${USE_HAL},1)
-    L+=/cluster/home/braney/hal/lib/halChain.a /cluster/home/braney/hal/lib/halLod.a /cluster/home/braney/hal/lib/halLib.a /cluster/home/braney/sonLib/lib/sonLib.a /hive/groups/recon/local/lib/libhdf5_cpp.a /hive/groups/recon/local/lib/libhdf5.a /hive/groups/recon/local/lib/libhdf5_hl.a /hive/groups/recon/local/lib/libsz.a -lstdc++
+    L+=${HALDIR}/hal/lib/halMaf.a ${HALDIR}/hal/lib/halChain.a ${HALDIR}/hal/lib/halMaf.a ${HALDIR}/hal/lib/halLiftover.a ${HALDIR}/hal/lib/halLod.a ${HALDIR}/hal/lib/halLib.a ${HALDIR}/sonLib/lib/sonLib.a ${HALDIR}/hdf5-1.8.11/hdf5//lib/libhdf5_cpp.a ${HALDIR}/hdf5-1.8.11/hdf5//lib/libhdf5.a ${HALDIR}/hdf5-1.8.11/hdf5//lib/libhdf5_hl.a 
     HG_DEFS+=-DUSE_HAL
-    HG_INC+=-I/cluster/home/braney/hal/chain/inc/
+    HG_INC+=-I${HALDIR}/hal/chain/inc/
 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