--- SeqLib/htslib/Makefile.orig	2017-06-20 12:40:28 UTC
+++ SeqLib/htslib/Makefile
@@ -22,20 +22,20 @@
 # 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
 
-CPPFLAGS =
+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 -D__FUNCTION__=__func__
-CFLAGS   = -g -Wall -O2
+CFLAGS   ?= -g -Wall -O2
 EXTRA_CFLAGS_PIC = -fpic
-LDFLAGS  =
+LDFLAGS  ?=
 LIBS     = $(htslib_default_libs)
 
 prefix      = /usr/local
@@ -86,7 +86,7 @@ BUILT_THRASH_PROGRAMS = \
 	test/thrash_threads5 \
 	test/thrash_threads6
 
-all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS)
+all: lib-static $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS)
 
 HTSPREFIX =
 include htslib_vars.mk