biology/pear-merger: Memory-efficient and accurate paired-end read merger

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D14959

biology/Makefile

@@ -78,6 +78,7 @@
     SUBDIR += p5-TrimGalore
     SUBDIR += p5-transdecoder
     SUBDIR += paml
+    SUBDIR += pear-merger
     SUBDIR += phrap
     SUBDIR += phred
     SUBDIR += phylip

biology/pear-merger/Makefile

@@ -0,0 +1,28 @@
+# $FreeBSD$
+
+# Newer versions require registration to download and the site is unreliable.
+
+PORTNAME=	pear
+DISTVERSION=	0.9.6
+CATEGORIES=	biology
+MASTER_SITES=	https://depot.galaxyproject.org/software/pear/
+PKGNAMESUFFIX=	-merger
+DISTNAME=	${PORTNAME}_${PORTVERSION}_src_all
+
+MAINTAINER=	jwb@FreeBSD.org
+COMMENT=	Memory-efficient and highly accurate paired-end read merger
+
+LICENSE=	CC-BY-NC-SA-3.0
+
+GNU_CONFIGURE=	yes
+
+WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}-src
+
+PLIST_FILES=	bin/pearRM man/man1/pearRM.1.gz
+
+do-install:
+	@${CP} ${WRKSRC}/man/pear.1 ${WRKSRC}/man/pearRM.1
+	${INSTALL_PROGRAM} ${WRKSRC}/src/pear ${STAGEDIR}${PREFIX}/bin/pearRM
+	${INSTALL_MAN} ${WRKSRC}/man/pearRM.1 ${STAGEDIR}${MANPREFIX}/man/man1
+
+.include <bsd.port.mk>

biology/pear-merger/distinfo

@@ -0,0 +1,3 @@
+TIMESTAMP = 1519766031
+SHA256 (pear_0.9.6_src_all.tar.gz) = f7728371e26a5b46fa928b0f7ae1b552ed6a78815b117ba48ef1af98e96c8e2b
+SIZE (pear_0.9.6_src_all.tar.gz) = 292790

biology/pear-merger/pkg-descr

@@ -0,0 +1,5 @@
+PEAR is an ultrafast, memory-efficient and highly accurate paired-end read
+merger. It is fully parallelized and can run with as low as just a few
+kilobytes of memory.
+
+WWW: http://sco.h-its.org/exelixis/web/software/pear/