--- a/Makefile	2017-03-13 09:55:48.000000000 -0500
+++ b/Makefile	2020-01-13 17:42:49.359554802 -0600
@@ -30,13 +30,14 @@
 
 # Adjust $(HTSDIR) to point to your top-level htslib directory
 HTSDIR = htslib-1.4
-include $(HTSDIR)/htslib.mk
-include $(HTSDIR)/htslib_static.mk
-HTSLIB = $(HTSDIR)/libhts.a
-BGZIP  = $(HTSDIR)/bgzip
-TABIX  = $(HTSDIR)/tabix
-HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS)
-HTSLIB_LIBS = $(HTSLIB_static_LIBS)
+#include $(HTSDIR)/htslib.mk
+#include $(HTSDIR)/htslib_static.mk
+HTSINC = $(HTSDIR)/include
+HTSLIB = -L$(HTSDIR)/lib -lhts
+BGZIP  = $(HTSDIR)/bin/bgzip
+TABIX  = $(HTSDIR)/bin/tabix
+#HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS)
+#HTSLIB_LIBS = $(HTSLIB_static_LIBS)
 
 CC       = gcc
 CPPFLAGS =
@@ -51,7 +52,7 @@
 endif
 
 # TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally
-ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
+ALL_CPPFLAGS = -I. -I$(HTSINC)
 ALL_LDFLAGS  = $(DYNAMIC_FLAGS) $(HTSLIB_LDFLAGS) $(LDFLAGS)
 ALL_LIBS     = -lm -lz -ldl $(LIBS)
 
@@ -64,7 +65,7 @@
            mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o \
            ccall.o em.o prob1.o kmin.o # the original samtools calling
 
-EXTRA_CPPFLAGS = -I. -I$(HTSDIR) -DPLUGINPATH=\"$(pluginpath)\"
+EXTRA_CPPFLAGS = -I. -I$(HTSINC) -DPLUGINPATH=\"$(pluginpath)\"
 GSL_LIBS       =
 
 # The polysomy command is not compiled by default because it brings dependency
@@ -73,7 +74,7 @@
 ifdef USE_GPL
     EXTRA_CPPFLAGS += -DUSE_GPL
     OBJS += polysomy.o peakfit.o
-    GSL_LIBS = -lgsl -lcblas
+    GSL_LIBS = -lgsl -lgslcblas
 endif
 
 prefix      = /usr/local
@@ -208,10 +209,10 @@
 
 test/test-regidx.o: test/test-regidx.c regidx.h
 
-test/test-regidx: test/test-regidx.o regidx.o $(HTSLIB)
+test/test-regidx: test/test-regidx.o regidx.o
 	$(CC) $(ALL_LDFLAGS) -o $@ $^ $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(ALL_LIBS)
 
-bcftools: $(HTSLIB) $(OBJS)
+bcftools: $(OBJS)
 	$(CC) $(ALL_LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(GSL_LIBS) $(ALL_LIBS)
 
 doc/bcftools.1: doc/bcftools.txt