9 files changed, 221 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index cca7466654dc..2f591aa84d19 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -66,6 +66,7 @@
     SUBDIR += paml
     SUBDIR += phd2fasta
     SUBDIR += phrap
+    SUBDIR += phred
     SUBDIR += phylip
     SUBDIR += platon
     SUBDIR += povchem
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} ${DOCSDIR}
+.endfor
+.endif
+
+.include <bsd.port.post.mk>
diff --git a/biology/phrap/distinfo b/biology/phrap/distinfo
new file mode 100644
index 000000000000..ad0d45f9a994
--- /dev/null
+++ b/biology/phrap/distinfo
@@ -0,0 +1,3 @@
+MD5 (phrap/distrib.tar.Z) = 35175595801cafd22ec348fb9dba0ce4
+SHA256 (phrap/distrib.tar.Z) = e0be79818e3a8ca17391f42cc0ffbaf1a63299c8845a0b9ac3aaeb3cac641fcc
+SIZE (phrap/distrib.tar.Z) = 366163
diff --git a/biology/phrap/files/patch-makefile b/biology/phrap/files/patch-makefile
new file mode 100644
index 000000000000..7fccdb3846a1
--- /dev/null
+++ b/biology/phrap/files/patch-makefile
@@ -0,0 +1,27 @@
+--- makefile.orig	1999-03-11 15:13:20.000000000 +0900
++++ makefile	2007-12-11 13:19:39.000000000 +0900
+@@ -23,8 +23,8 @@
+ #*****************************************************************************/
+ 
+ # Makefile for swat, phrap, cross_match, phrapview; also swprobs (currently inactivated)
+-CC= cc
+-CFLAGS= -O2
++CC?= cc
++#CFLAGS= -O2
+ LFLAGS= -lm
+ 
+ SWATOBJS= swat.o weibull.o
+@@ -55,11 +55,11 @@
+ 
+ manyreads:  
+ 	touch swat.h;
+-	make CFLAGS="-O2 -DMANYREADS" phrap cross_match;
++	make CFLAGS="$(CFLAGS) -DMANYREADS" phrap cross_match;
+ 	mv phrap phrap.manyreads;
+ 	mv cross_match cross_match.manyreads;
+ 	touch swat.h;
+-	make CFLAGS="-O2 -DLONGREADS" phrap;
++	make CFLAGS="$(CFLAGS) -DLONGREADS" phrap;
+ 	mv phrap phrap.longreads;
+ 	touch swat.h;
+ 	make phrap cross_match;
diff --git a/biology/phrap/pkg-descr b/biology/phrap/pkg-descr
new file mode 100644
index 000000000000..d8d44bb5d37c
--- /dev/null
+++ b/biology/phrap/pkg-descr
@@ -0,0 +1,21 @@
+Phrap is a program for assembling shotgun DNA sequence data.
+Among other features, it allows use of the entire read and not just the
+trimmed high quality part, it uses a combination of user-supplied and
+internally computed data quality information to improve assembly accuracy
+in the presence of repeats, it constructs the contig sequence as a mosaic
+of the highest quality read segments rather than a consensus, it provides
+extensive assembly information to assist in trouble-shooting assembly
+problems, and it handles large datasets.
+
+This package also contains Swat and Cross_match.
+Swat is a program for searching one or more DNA or protein query sequences
+against a sequence database, using (an efficient implementation of) the
+Smith-Waterman-Gotoh algorithm.
+Cross_Match is a general-purpose utility based on Swat for comparing any
+two sets of DNA sequences, and it can be used to:
+* produce vector-masked versions of a set of reads
+* compare a set of cDNA sequences to a set of cosmids
+* compare contigs found by two altanative assembly procedures to each other
+* compare phrap contigs to the final edited cosmid sequence.
+
+WWW: http://www.phrap.org/phredphrapconsed.html
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