--- kent/src/submodules/htslib/Makefile.orig	2026-08-30 18:17:35 UTC
+++ kent/src/submodules/htslib/Makefile
@@ -22,9 +22,9 @@
 # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 # DEALINGS IN THE SOFTWARE.
 
-CC     = gcc
-AR     = ar
-RANLIB = ranlib
+CC     ?= gcc
+AR     ?= ar
+RANLIB ?= ranlib
 
 # Default libraries to link if configure is not used
 htslib_default_libs = -lz -lm -lbz2 -llzma -lcurl
@@ -35,14 +35,14 @@ CPPFLAGS =
 # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
 # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
 #CFLAGS   = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600
-CFLAGS   = -g -Wall -O2 -fvisibility=hidden
+CFLAGS   ?= -g -Wall -O2 -fvisibility=hidden
 EXTRA_CFLAGS_PIC = -fpic
 TARGET_CFLAGS =
-LDFLAGS  = -fvisibility=hidden
+LDFLAGS  ?= -fvisibility=hidden
 VERSION_SCRIPT_LDFLAGS = -Wl,-version-script,$(srcprefix)htslib.map
 LIBS     = $(htslib_default_libs)
 
-prefix      = /usr/local
+prefix      = ${PREFIX}
 exec_prefix = $(prefix)
 bindir      = $(exec_prefix)/bin
 includedir  = $(prefix)/include