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>

4 files changed, 107 insertions, 0 deletions

diff --git a/biology/phred/Makefile b/biology/phred/Makefile
new file mode 100644
index 000000000000..43f3040cf016
--- /dev/null
+++ b/biology/phred/Makefile
@@ -0,0 +1,67 @@
+# New ports collection makefile for:	phred
+# Date created:		6 December 2007
+# Whom:			Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	phred
+PORTVERSION=	0.020425.c
+CATEGORIES=	biology
+MASTER_SITES=	# put the tarball manually
+DISTNAME=	${PORTNAME}-dist-${PORTVERSION:S/0.//}-acd
+EXTRACT_SUFX=	.tar.Z
+
+MAINTAINER=	mzaki@biol.s.u-tokyo.ac.jp
+COMMENT=	Base calling and quality value assignment on DNA sequencing
+
+RESTRICTED=	Redistribution is not permitted in any form. You must request the tarball via e-mail. Free for academic use.
+
+NO_WRKSUBDIR=	yes
+
+ALL_TARGET=	phred daev
+
+BINMODE=	0111	# avoid copying binaries as required by the agreement
+BINARIES=	phred daev
+.for f in ${BINARIES}
+PLIST_FILES+=	bin/${f}
+.endfor
+
+DATADIR=	${PREFIX}/etc/PhredPar
+DATAFILES=	phredpar.dat
+.for f in ${DATAFILES}
+PORTDATA+=	${f}.dist
+.endfor
+
+PORTDOCS=	NEWS PHRED.DOC DAEV.DOC
+
+.include <bsd.port.pre.mk>
+
+.for f in ${DISTFILES}
+.if !exists(${DISTDIR}/${f})
+IGNORE=	you must request the source code \(${f}\) via e-mail, place it manually in ${DISTDIR}, and then try it again
+.endif
+.endfor
+
+do-install:
+.for f in ${BINARIES}
+	@${INSTALL_PROGRAM} ${WRKSRC}/${f} ${PREFIX}/bin/
+.endfor
+	@${MKDIR} ${DATADIR}
+.for f in ${DATAFILES}
+	@${INSTALL_DATA} ${WRKSRC}/${f} ${DATADIR}/${f}.dist
+.endfor
+.if !defined(NOPORTDOCS)
+	@${MKDIR} ${DOCSDIR}
+.for f in ${PORTDOCS}
+	@${INSTALL_DATA} ${WRKSRC}/${f} ${DOCSDIR}
+.endfor
+.endif
+	@${ECHO} "---------------------------------------------------------------------------"
+	@${ECHO} "You must set PHRED_PARAMETER_FILE environment variable."
+	@${ECHO} ""
+	@${ECHO} "The default parameter file in the distribution is located at:"
+	@${ECHO} "  ${DATADIR}/phredpar.dat.dist"
+	@${ECHO} "---------------------------------------------------------------------------"
+
+.include <bsd.port.post.mk>
diff --git a/biology/phred/distinfo b/biology/phred/distinfo
new file mode 100644
index 000000000000..f2b0720d585d
--- /dev/null
+++ b/biology/phred/distinfo
@@ -0,0 +1,3 @@
+MD5 (phred-dist-020425.c-acd.tar.Z) = f6f86e14b6283d4797a5872a8d44a358
+SHA256 (phred-dist-020425.c-acd.tar.Z) = c7a7773447376c024212b680e1ce1e52c30ad8e18dee317ba863bc10db94f6c9
+SIZE (phred-dist-020425.c-acd.tar.Z) = 547645
diff --git a/biology/phred/files/patch-Makefile b/biology/phred/files/patch-Makefile
new file mode 100644
index 000000000000..244e284a9f94
--- /dev/null
+++ b/biology/phred/files/patch-Makefile
@@ -0,0 +1,13 @@
+--- Makefile.orig	2002-07-27 07:22:10.000000000 +0900
++++ Makefile	2007-12-06 16:41:35.000000000 +0900
+@@ -12,8 +12,8 @@
+ 
+ # UNIX specific definitions (default)
+ #
+-CC= cc
+-CFLAGS= -O -DANSI_C $(LXFLAGS)
++CC?= cc
++CFLAGS+= -DANSI_C $(LXFLAGS)
+ CLIB= -lm
+ 
+ # Windows 'nmake' specific definitions
diff --git a/biology/phred/pkg-descr b/biology/phred/pkg-descr
new file mode 100644
index 000000000000..b92feefd076a
--- /dev/null
+++ b/biology/phred/pkg-descr
@@ -0,0 +1,24 @@
+Phred reads DNA sequencer trace data, calls bases, assigns quality values
+to the bases, and writes the base calls and quality values to output files.
+
+Trace data is read from chromatogram files in the SCF, ABI, and EST formats,
+even if they were compressed using gzip, bzip2, or UNIX compress.
+Quality values are written to FASTA format files or PHD files, which can be
+used by the Phrap sequence assembly program in order to increase the accuracy
+of the assembled sequence.
+
+Base calling and quality value accuracies tested for:
+  ABI models 373, 377, and 3700
+  Molecular Dynamics MegaBACE
+  LI-COR 4000
+
+Base calling accuracies tested for:
+  ABI model 3100
+  Beckman CEQ
+
+It contains also a data evaluation program called 'daev'.
+See DAEV.DOC for more information.
+
+You must obtain the tarball via e-mail to build. See the web site below.
+
+WWW: http://www.phrap.org/phredphrapconsed.html