1 files changed, 56 insertions, 0 deletions

diff --git a/biology/ncbi-blast+/Makefile b/biology/ncbi-blast+/Makefile
new file mode 100644
index 000000000000..e056a5811a10
--- /dev/null
+++ b/biology/ncbi-blast+/Makefile
@@ -0,0 +1,56 @@
+# Created by: Jason Bacon <jwbacon@tds.net>
+# $FreeBSD$
+
+PORTNAME=	blast+
+PORTVERSION=	2.2.30
+CATEGORIES=	biology
+MASTER_SITES=	http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/
+PKGNAMEPREFIX=	ncbi
+DISTNAME=	ncbi-blast-${PORTVERSION}+-src
+
+MAINTAINER=	jwbacon@tds.net
+COMMENT=	NCBI implementation of Basic Local Alignment Search Tool
+
+LICENSE=	Public_domain
+LICENSE_NAME=	Public Domain
+LICENSE_FILE=	${WRKSRC}/scripts/projects/blast/LICENSE
+LICENSE_PERMS=	dist-mirror dist-sell pkg-mirror pkg-sell auto-accept
+
+LIB_DEPENDS=	libpcre.so:${PORTSDIR}/devel/pcre \
+		libbz2.so:${PORTSDIR}/archivers/bzip2
+
+WRKSRC=		${WRKDIR}/${DISTNAME}/c++
+
+GNU_CONFIGURE=	yes
+USES=		gmake shebangfix perl5 python
+SHEBANG_FILES=	src/app/blast/legacy_blast.pl \
+		src/app/blast/update_blastdb.pl \
+		src/app/winmasker/windowmasker_2.2.22_adapter.py
+
+# Requires openmp
+USE_GCC=	yes
+USE_LDCONFIG=	yes
+
+# The test for amq can hang, but amq is not needed so just avoid the test
+CONFIGURE_ENV=	ncbi_cv_prog_amq_w=no
+
+# configure chooses /usr/local/bin/ar with no flags
+# FreeBSD boost port flagged by configure as untested version
+CONFIGURE_ARGS+=AR="ar cr" --without-boost
+
+# Fix "undefined _ThreadRuneLocale" error on 10.0
+# Fix unknown options in configure
+# Add staging support to configure-generated Makefile
+post-patch:
+	${REINPLACE_CMD} \
+		-e 's|-D_THREAD_SAFE|-D_THREAD_SAFE -D__RUNETYPE_INTERNAL|' \
+		-e '/--infodir=DIR/d' \
+		-e '/--mandir=DIR/d' \
+		${WRKSRC}/src/build-system/configure
+	${REINPLACE_CMD} -e 's|@prefix@|${STAGEDIR}@prefix@|g' \
+		${WRKSRC}/src/build-system/Makefile.in.top
+
+post-install:
+	${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/*.so
+
+.include <bsd.port.mk>