gemma: Clean up, test with new blas infrastructure

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Wed May 29 16:30:26 2019 -0500
Changeset:	dc530c5e655cf181fb0726fa26764b7f50b2a7c1

Modified Files:
	gemma/Makefile

Log Message:
gemma: Clean up, test with new blas infrastructure

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=dc530c5e655cf181fb0726fa26764b7f50b2a7c1

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 gemma/Makefile | 29 +++++++++++++++++++++--------
 1 file changed, 21 insertions(+), 8 deletions(-)

diffs:
diff --git a/gemma/Makefile b/gemma/Makefile
index 2c599b57e6..2d6574abaa 100644
--- a/gemma/Makefile
+++ b/gemma/Makefile
@@ -5,31 +5,44 @@
 #              Mon Apr 29 11:01:43 CDT 2019               #
 ###########################################################
 
-DISTNAME=	GEMMA-${PV}
+DISTNAME=	GEMMA-0.98.1
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=genetics-statistics/}
 GITHUB_PROJECT=	GEMMA
-GITHUB_TAG=	${PV}
 
 MAINTAINER=	bacon%NetBSD.org@localhost
 HOMEPAGE=	https://github.com/genetics-statistics/GEMMA
 COMMENT=	Genome-wide Efficient Mixed Model Association
 LICENSE=	gnu-gpl-v3
 
-# Just assuming C and C++: Adjust this!
 USE_LANGUAGES=	c c++
 USE_TOOLS+=	gmake
 
-CXXFLAGS+=	-I${PREFIX}/include/eigen3 -DOPENBLAS -DOPENBLAS_LEGACY
+CXXFLAGS+=	-I${PREFIX}/include/eigen3
 CXXFLAGS+=	-fpermissive
-MAKE_FLAGS+=	LDFLAGS+="${BLAS_LIBS} -lgsl -lcblas -lz"
+MAKE_FLAGS+=	LDFLAGS+="${LAPACK_LIBS} -lgsl -lcblas -lz"
 MAKE_FILE=	${FILESDIR}/Makefile
 
-PV=		0.98.1
-BLAS_ACCEPTED=	openblas	# Unusably slow with netlib
+# Requires multithreading for decent performance
+BLAS_ACCEPTED=	openblas_pthread openblas_openmp
 
-.include "../../devel/zlib/buildlink3.mk"
 .include "../../wip/mk/blas.buildlink3.mk"
+
+.if !empty(BLAS_TYPE:Mopenblas*)
+CXXFLAGS+=	-I${PREFIX}/include/${BLAS_TYPE} -DOPENBLAS
+.endif
+
+# No multithreading
+.if ${BLAS_TYPE} == "openblas"
+CXXFLAGS+=	-DOPENBLAS_LEGACY
+.endif
+
+INSTALLATION_DIRS=	bin share/examples
+
+do-test:
+	(cd ${WRKSRC}/test && ${SH} test_suite.sh)
+
+.include "../../devel/zlib/buildlink3.mk"
 .include "../../wip/cblas/buildlink3.mk"
 .include "../../math/gsl/buildlink3.mk"
 .include "../../math/eigen3/buildlink3.mk"