Static compilation

Makefile.am

@@ -1,7 +1,7 @@
 ACLOCAL_AMFLAGS = -I m4
 
 AM_CPPFLAGS = -std=c++11 $(BOOST_CPPFLAGS) $(EIGEN_CFLAGS) $(JELLYFISH_CFLAGS) $(HTSLIB_CFLAGS) $(GSL_CFLAGS) $(GUROBI_CFLAGS) $(CLP_CFLAGS) -fopenmp
-AM_LDFLAGS = $(BOOST_IOSTREAMS_LDFLAGS) $(HTSLIB_LDFLAGS) $(JELLYFISH_LDFLAGS) $(GSL_LDFLAGS) $(GUROBI_LDFLAGS) $(CLP_CFLAGS) -fopenmp
+AM_LDFLAGS = $(BOOST_IOSTREAMS_LDFLAGS) $(HTSLIB_LDFLAGS) $(JELLYFISH_LDFLAGS) $(GSL_LDFLAGS) $(GUROBI_LDFLAGS) $(CLP_LDFLAGS) $(STATIC_FLAGS) -fopenmp
 LIBS = $(BOOST_IOSTREAMS_LIBS)  $(HTSLIB_LIBS) $(GSL_LIBS) $(GUROBI_LIBS) $(CLP_LIBS) -lz -lm -fopenmp
 
 EXTRA_DIST = src/spline.h src/logtime.hpp src/massert.hpp install-dependencies.sh

configure.ac

@@ -13,6 +13,15 @@ PKG_PROG_PKG_CONFIG
 AC_LANG(C++)
 AC_PROG_CXX
 
+# --enable-all-static
+# Do not use libtool if building all static
+AC_ARG_ENABLE([all-static],
+              [AC_HELP_STRING([--enable-all-static], [create statically linked executable])])
+STATIC_FLAGS=
+AS_IF([test x$enable_all_static = xyes],
+      [AC_SUBST([STATIC_FLAGS], [-all-static])]
+      [PKG_CONFIG="$PKG_CONFIG --static"])
+
 # Boost
 BOOST_REQUIRE
 BOOST_STATIC
@@ -38,12 +47,14 @@ PKG_CHECK_MODULES([JELLYFISH], [jellyfish-2.0])
 PKG_CHECK_MODULES([HTSLIB], [htslib])
 PKG_CHECK_MODULES([GSL], [gsl])
 
+
 # Extra RPATH stuff?
-AC_LIB_LINKFLAGS_FROM_LIBS([JELLYFISH_LDFLAGS], [$JELLYFISH_LIBS])
-AC_LIB_LINKFLAGS_FROM_LIBS([HTSLIB_LDFLAGS], [$HTSLIB_LIBS])
-AC_LIB_LINKFLAGS_FROM_LIBS([GSL_LDFLAGS], [$GSL_LIBS])
-AC_LIB_LINKFLAGS_FROM_LIBS([GUROBI_LDFLAGS], [$GUROBI_LIBS])
-AC_LIB_LINKFLAGS_FROM_LIBS([CLP_LDFLAGS], [$CLP_LIBS])
+AS_IF([test x$enable_all_static != xyes],
+      [AC_LIB_LINKFLAGS_FROM_LIBS([JELLYFISH_LDFLAGS], [$JELLYFISH_LIBS])]
+      [AC_LIB_LINKFLAGS_FROM_LIBS([HTSLIB_LDFLAGS], [$HTSLIB_LIBS])]
+      [AC_LIB_LINKFLAGS_FROM_LIBS([GSL_LDFLAGS], [$GSL_LIBS])]
+      [AC_LIB_LINKFLAGS_FROM_LIBS([GUROBI_LDFLAGS], [$GUROBI_LIBS])]
+      [AC_LIB_LINKFLAGS_FROM_LIBS([CLP_LDFLAGS], [$CLP_LIBS])])
 
 AC_CONFIG_FILES([Makefile])
 AC_OUTPUT

install-dependencies.sh

@@ -68,7 +68,7 @@ else
 	tar -xjvf htslib-1.9.tar.bz2
 	cd ${Dir}/external/htslib-1.9/
 	mkdir -p Installation
-	./configure --prefix=${Dir}/external/htslib-1.9/Installation
+	./configure --prefix=${Dir}/external/htslib-1.9/Installation --enable-plugins=no --enable-libcurl=no --enable-s3=no
 	make
 	make install
         cp $(find ${Dir}/external/htslib-1.9/Installation -name *.pc) ${Dir}/external/pkgconfig/
@@ -102,7 +102,7 @@ else
 	tar -zxf Clp-1.17.5.tgz
 	cd Clp-1.17.5/
 	mkdir -p Installation
-	./configure -C --prefix=${Dir}/external/Clp-1.17.5/Installation
+	./configure -C --prefix=${Dir}/external/Clp-1.17.5/Installation --enable-static
 	make
 	make install
         cp $(find ${Dir}/external/Clp-1.17.5/Installation -name *.pc) ${Dir}/external/pkgconfig/
@@ -117,4 +117,4 @@ echo
 echo "To configure with CLP, run: ./configure PKG_CONFIG_PATH=${PKG_CONFIG_PATH} BOOST_ROOT=${Dir}/external/boost_1_69_0/Installation"
 echo "To configure with gurobi, run: ./configure PKG_CONFIG_PATH=${PKG_CONFIG_PATH} --with-gurobi=<path to gurobi linux64 folder> BOOST_ROOT=${Dir}/external/boost_1_69_0/Installation"
 echo
-echo "Then compile and install with: make install
+echo "Then compile and install with: make install"