--- Makefile    2018-03-03 21:35:11.450748318 +0000
+++ Makefile    2018-03-12 22:26:32.603369889 +0000
@@ -8,7 +8,7 @@
 #

 #Basic flags every build needs
-LIBS=-lz
+LIBS=-lcrypto -lz -llzma -lbz2 -lcurl
 CXXFLAGS ?= -g -O3
 CXXFLAGS += -std=c++11 -fopenmp -fsigned-char
 CFLAGS ?= -O3 -std=c99
@@ -46,19 +46,8 @@
     EIGEN_CHECK=
 endif

-# Default to build and link the libhts submodule
-ifeq ($(HTS), install)
-    HTS_LIB=./htslib/libhts.a
-    HTS_INCLUDE=-I./htslib
-else
-    # Use system-wide htslib
-    HTS_LIB=
-    HTS_INCLUDE=
-    LIBS += -lhts
-endif
-
 # Include the header-only fast5 library
-FAST5_INCLUDE=-I./fast5/include
+#FAST5_INCLUDE=-I./fast5/include

 # Include the header-only eigen library
 EIGEN_INCLUDE=-I./eigen/
--- src/nanopolish_methyltrain.cpp    2018-03-03 21:35:35.230748318 +0000
+++ src/nanopolish_methyltrain.cpp    2018-03-03 21:35:58.920748318 +0000
@@ -42,7 +42,7 @@
 #include "logger.hpp"

 #include "nanopolish_scorereads.h"
-#include "Eigen/Dense"
+#include <eigen3/Eigen/Dense>

 extern float g_p_skip, g_p_skip_self, g_p_bad, g_p_bad_self;

