diff --git a/biology/gcta/Makefile b/biology/gcta/Makefile
index 67afd90d9a71..37f0edc6cc84 100644
--- a/biology/gcta/Makefile
+++ b/biology/gcta/Makefile
@@ -1,27 +1,33 @@
 PORTNAME=	gcta
 DISTVERSION=	1.26.0
 PORTREVISION=	3
 CATEGORIES=	biology
-MASTER_SITES=	https://cnsgenomics.com/software/gcta/pre_gcta/
-DISTNAME=	${PORTNAME}_${PORTVERSION}_src
+MASTER_SITES=	https://cnsgenomics.com/software/gcta/pre_gcta/:main \
+		https://gitlab.com/libeigen/eigen/-/archive/${EIGEN_VERSION}/:eigen
+DISTFILES=	${PORTNAME}_${DISTVERSION}_src${EXTRACT_SUFX}:main \
+		eigen-${EIGEN_VERSION}.tar.gz:eigen
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Genome-wide Complex Trait Analysis
 
 LICENSE=	GPLv3
 LICENSE_FILE=	${WRKSRC}/GNU_General_Public_License_v3.txt
 
 LIB_DEPENDS=	libopenblas.so:math/openblas
 
-USES=		compiler:c++11-lang dos2unix eigen:3 gmake localbase:ldflags zip
+USES=		compiler:c++11-lang dos2unix gmake localbase:ldflags zip
 
-CXXFLAGS+=	-I${LOCALBASE}/include/eigen3 -fopenmp
+CXXFLAGS+=	-I${WRKDIR}/eigen-${EIGEN_VERSION} -fopenmp
 LDFLAGS+=	-lopenblas
 
 INSTALL_TARGET=	install-strip
 PLIST_FILES=	bin/gcta
 
+EIGEN_VERSION=	3.3.9
+
 do-extract:
-	${UNZIP_NATIVE_CMD} -d ${WRKSRC} ${DISTDIR}/${DISTFILES}
+	@${UNZIP_NATIVE_CMD} -d ${WRKSRC} ${DISTDIR}/${PORTNAME}_${DISTVERSION}_src${EXTRACT_SUFX}
+	@cd ${WRKDIR} && \
+		${TAR} xzf ${DISTDIR}/eigen-${EIGEN_VERSION}.tar.gz
 
 .include <bsd.port.mk>
diff --git a/biology/gcta/distinfo b/biology/gcta/distinfo
index 9faabb4559b8..91c72879eac1 100644
--- a/biology/gcta/distinfo
+++ b/biology/gcta/distinfo
@@ -1,3 +1,5 @@
-TIMESTAMP = 1489125670
+TIMESTAMP = 1657137653
 SHA256 (gcta_1.26.0_src.zip) = 554c48f421c93cbaf64b1c300ca507d8e7a56086b5c7d857227fbd4048f42acf
 SIZE (gcta_1.26.0_src.zip) = 198045
+SHA256 (eigen-3.3.9.tar.gz) = 7985975b787340124786f092b3a07d594b2e9cd53bbfe5f3d9b1daee7d55f56f
+SIZE (eigen-3.3.9.tar.gz) = 2142379