--- emboss-6.3.1_p4-r1.ebuild.ori	2012-02-02 18:16:51.000000000 +0100
+++ emboss-6.3.1_p4-r1.ebuild.ori	2012-02-02 18:27:07.000000000 +0100
@@ -4,7 +4,7 @@ 
 
 EAPI="4"
 
-inherit emboss
+inherit emboss autotools
 
 EBO_PATCH="4"
 EBOV=${PV/_p*}
@@ -42,6 +42,9 @@ 
 	#epatch emboss-6.3.1_p4-r1_plcol.patch
 	epatch "${FILESDIR}/plcol.patch"
 	emboss_src_prepare
+	sed -i 's/CFLAGS -O2/CFLAGS/g' "${S}"/configure.in || die
+	eautomake
+	eautoreconf
 }
 
 src_install() {