New port: biology/consed viewing and editing workbench for sequence

assembly

	Consed is a tool for viewing, editing, and finishing sequence
	assemblies.

	The port is constituted of 4 parts:
	biology/phred: base caller with quality evaluation
	biology/phrap: sequence assembler for shotgun sequencing
	biology/consed: workbench
	biology/phd2fasta: small utility

	All these can be used separately; however, most function
	of consed depends on the others.

	Although these programs are licensed freely for academic
	and nonprofit purposes, users have to contact the authors
	to get the softwares.
	Phred (including phd2fasta) and phrap are emailed,
	and consed can be downloaded to a restricted IP address.
	For commercial users, the licensing fee is ca. $10,000 at
	the time of writing.

PR:		ports/118548
Submitted by:	Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>

1 files changed, 62 insertions, 0 deletions

diff --git a/biology/phrap/Makefile b/biology/phrap/Makefile
new file mode 100644
index 000000000000..094d772390aa
--- /dev/null
+++ b/biology/phrap/Makefile
@@ -0,0 +1,62 @@
+# New ports collection makefile for:	phrap
+# Date created:		21 June 2005
+# Whom:			Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	phrap
+PORTVERSION=	0.990329
+CATEGORIES=	biology
+MASTER_SITES=	# put the tarball manually
+DISTFILES=	distrib.tar.Z
+DIST_SUBDIR=	${PORTNAME}
+
+MAINTAINER=	mzaki@biol.s.u-tokyo.ac.jp
+COMMENT=	Phrap is a program for assembling shotgun DNA sequence data
+
+RESTRICTED=	Redistribution is not permitted in any form. You must request the tarball via e-mail. Free for academic use.
+
+NO_WRKSUBDIR=	yes
+
+MAKEFILE=	makefile
+ALL_TARGET=	all manyreads
+
+BINARIES=	cluster cross_match cross_match.manyreads loco \
+		phrap phrap.longreads phrap.manyreads swat
+SCRIPTS=	phrapview
+.for f in ${BINARIES} ${SCRIPTS}
+PLIST_FILES+=	bin/${f}
+.endfor
+
+PORTDATA=	BLOSUM50 BLOSUM62 PAM250 mat50 mat70 penalty2 vector.seq
+PORTDOCS=	general.doc phrap.doc swat.doc
+
+.include <bsd.port.pre.mk>
+
+.for f in ${DISTFILES}
+.if !exists(${DISTDIR}/${DIST_SUBDIR}/${f})
+IGNORE=	you must request the source code \(${DISTFILES}\) via e-mail, place it manually in ${DISTDIR}/${DIST_SUBDIR}, and then try it again
+.endif
+.endfor
+
+do-install:
+.for f in ${BINARIES}
+	@${INSTALL_PROGRAM} ${WRKSRC}/${f} ${PREFIX}/bin/
+	@${CHMOD} a-r ${PREFIX}/bin/${f} # as required by the agreement
+.endfor
+.for f in ${SCRIPTS}
+	@${INSTALL_SCRIPT} ${WRKSRC}/${f} ${PREFIX}/bin/
+.endfor
+	@${MKDIR} ${DATADIR}
+.for f in ${PORTDATA}
+	@${INSTALL_DATA} ${WRKSRC}/${f} ${DATADIR}
+.endfor
+.if !defined(NOPORTDOCS)
+	@${MKDIR} ${DOCSDIR}
+.for f in ${PORTDOCS}
+	@${INSTALL_DATA} ${WRKSRC}/${f} ${DOCSDIR}
+.endfor
+.endif
+
+.include <bsd.port.post.mk>