Add blast, a powerful software package for gene and protein identification,

using sensitive, selective and rapid similarity searches of protein and
nucleotide sequence databases.

PR:		ports/69636
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>

7 files changed, 325 insertions, 0 deletions

diff --git a/LEGAL b/LEGAL
index 8aea236a74ea..d566ea13cd33 100644
--- a/LEGAL
+++ b/LEGAL
@@ -61,6 +61,7 @@ BCWipe-*		ports/security/bcwipe	Non-Commercial Distribution and
 						Use Only
 bicom*			ports/archivers/bicom	Contact author personally
 						regarding commercial use
+blast-freebsd*		ports/biology/blast	Must be downloaded from vendor site
 bnetd			ports/games/bnetd	has been disabled for legal issue
 bomb.tar.gz		ports/games/bomb	mixture of GPL and X license
 boodler-*		ports/audio/boodler	not for commercial use
diff --git a/biology/Makefile b/biology/Makefile
index 37da8a15a1cc..fee70f22165f 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -10,6 +10,7 @@
     SUBDIR += avida
     SUBDIR += babel
     SUBDIR += biojava
+    SUBDIR += blast
     SUBDIR += chemeq
     SUBDIR += clustalw
     SUBDIR += coalesce
diff --git a/biology/blast/Makefile b/biology/blast/Makefile
new file mode 100644
index 000000000000..359c153f1be9
--- /dev/null
+++ b/biology/blast/Makefile
@@ -0,0 +1,77 @@
+# New ports collection makefile for:	WU BLAST
+# Date created:		27 May 2004
+# Whom:	      		Fernan Aguero <fernan@iib.unsam.edu.ar>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	wu-blast
+PORTVERSION=	2.0
+CATEGORIES=	biology
+MASTER_SITES=	#
+EXTRACT_SUFX=	.tar.Z
+
+MAINTAINER=	fernan@iib.unsam.edu.ar
+COMMENT=	WU BLAST, a software package for sequence similarity searches
+
+RESTRICTED=	"License does not allow redistribution of binaries. You should first register for the software, which is free for academic use."
+ONLY_FOR_ARCHS=	i386
+
+NO_BUILD=	yes
+DOWNLOAD_URL=	http://blast.wustl.edu/licensing
+
+NO_WRKSUBDIR=	yes
+PKGMESSAGE=	${WRKDIR}/pkg-message
+
+PORTDOCS=	COPYRIGHT FAQ-Indexing.html HISTORY LICENSE Memory.html \
+		README.html parameters.html
+BINS=		blasta gb2fasta gt2fasta memfile nrdb pam patdb \
+		pir2fasta sp2fasta xdformat xdget
+SCRIPTS=	wu-blastall wu-formatdb
+BLASTA_LINKS=	blastn blastp blastx tblastn tblastx
+XDFORMAT_LINKS=	setdb pressdb
+
+.include <bsd.port.pre.mk>
+
+.if ${OSVERSION} < 500000
+DISTNAME=	blast${PORTVERSION:S/.0//}.freebsd-4.x-i686
+.else
+DISTNAME=	blast${PORTVERSION:S/.0//}.freebsd-i686
+.endif
+
+.if !exists(${DISTDIR}/${DISTNAME}${EXTRACT_SUFX})
+IGNORE=	"You must manually fetch ${PORTNAME}${PORTVERSION:S/.0//} for the FreeBSD platform \(${DISTNAME}${EXTRACT_SUFX}\) from ${DOWNLOAD_URL}, place it in ${DISTDIR} and then run make again"
+.endif
+
+post-patch:
+	@${SED} -e 's,%%DATADIR%%,${DATADIR},g' < ${FILESDIR}/pkg-message.in > ${PKGMESSAGE}
+
+do-install:
+.for bin in ${BINS}
+	${INSTALL_PROGRAM} ${WRKSRC}/${bin} ${PREFIX}/bin
+.endfor
+.for script in ${SCRIPTS}
+	${INSTALL_SCRIPT} ${WRKSRC}/${script} ${PREFIX}/bin
+.endfor
+	${CHMOD} a-rw,a+x ${PREFIX}/bin/blasta
+.for blink in ${BLASTA_LINKS}
+	@(cd ${PREFIX}/bin && ${LN} -s blasta ${blink})
+.endfor
+.for xlink in ${XDFORMAT_LINKS}
+	@(cd ${PREFIX}/bin && ${LN} -s xdformat ${xlink})
+.endfor
+.if !defined (NOPORTDOCS)
+	@${MKDIR} ${DOCSDIR}
+.for doc in ${PORTDOCS}
+	${INSTALL_MAN} ${WRKSRC}/${doc} ${DOCSDIR}
+.endfor
+.endif
+	${MKDIR} ${DATADIR}
+	${CP} -R ${WRKSRC}/matrix ${DATADIR}
+	${CP} -R ${WRKSRC}/filter ${DATADIR}
+	${CP} ${WRKSRC}/sysblast.sample ${DATADIR}
+
+post-install:
+	@${CAT} ${PKGMESSAGE}
+
+.include <bsd.port.post.mk>
diff --git a/biology/blast/distinfo b/biology/blast/distinfo
new file mode 100644
index 000000000000..14ac62ecc56c
--- /dev/null
+++ b/biology/blast/distinfo
@@ -0,0 +1,4 @@
+MD5 (blast2.freebsd-4.x-i686.tar.Z) = c976f97f739d83a7a14a7cead81a64af
+MD5 (blast2.freebsd-i686.tar.Z) = 839aaf78e669fb895aa1f39b49a497be
+SIZE (blast2.freebsd-4.x-i686.tar.Z) = 1546671
+SIZE (blast2.freebsd-i686.tar.Z) = 1589046
diff --git a/biology/blast/files/pkg-message.in b/biology/blast/files/pkg-message.in
new file mode 100644
index 000000000000..c2fa0c29be37
--- /dev/null
+++ b/biology/blast/files/pkg-message.in
@@ -0,0 +1,15 @@
+======================================================================
+
+A sample configuration file has been installed in %%DATADIR%% and named
+sysblast.sample. Edit it to suit your needs, rename it to 'sysblast' and
+place it under /etc so that it can be recognized at runtime by the blast
+executable.
+
+Matrix files and filter executables have been placed in 
+%%DATADIR%%/matrix and %%DATADIR%%/filter, respectively. 
+You should set environment variables WUBLASTMAT and WUBLASTFILTER
+(pointing to the respective directories) so that the blast executable
+can find them.
+
+======================================================================
+
diff --git a/biology/blast/pkg-descr b/biology/blast/pkg-descr
new file mode 100644
index 000000000000..902e6fbcb5be
--- /dev/null
+++ b/biology/blast/pkg-descr
@@ -0,0 +1,18 @@
+Washington University BLAST (WU BLAST) version 2.0 is a powerful
+software package for gene and protein identification, using sensitive,
+selective and rapid similarity searches of protein and nucleotide
+sequence databases. WU BLAST 2.0 builds upon WU BLAST 1.4, which in turn
+was based on the public domain NCBI BLAST version 1.4. While NCBI BLAST
+and WU BLAST 1.4 are in the public domain, WU BLAST 2.0 contains
+significant new features and extended capabilities, the development of
+which began in late 1994, at Washington University in Saint Louis. First
+released in May 1996, or more than a year ahead of the NCBI, WU BLAST
+2.0 is the original gapped BLAST with statistics and is known for
+setting higher standards for sensitivity, speed, correctness and
+accuracy, scalability and reliability than competing programs and
+implementations. WU BLAST is neither a re-hashed nor "Mac-ified" version
+of NCBI BLAST, although WU BLAST in many ways is easier to use. WU BLAST
+essentially shares no code with NCBI BLAST, except for portions that
+both packages derived from ungapped NCBI BLAST 1.4.
+
+WWW: http://blast.wustl.edu
diff --git a/biology/blast/pkg-plist b/biology/blast/pkg-plist
new file mode 100644
index 000000000000..f2cd7d967d37
--- /dev/null
+++ b/biology/blast/pkg-plist
@@ -0,0 +1,209 @@
+bin/blasta
+bin/gb2fasta
+bin/gt2fasta
+bin/memfile
+bin/nrdb
+bin/pam
+bin/patdb
+bin/pir2fasta
+bin/sp2fasta
+bin/xdformat
+bin/xdget
+bin/wu-blastall
+bin/wu-formatdb
+bin/blastn
+bin/blastp
+bin/blastx
+bin/tblastn
+bin/tblastx
+bin/setdb
+bin/pressdb
+%%DATADIR%%/matrix/aa/nuc.4.4
+%%DATADIR%%/matrix/aa/BLOSUM30
+%%DATADIR%%/matrix/aa/BLOSUM35
+%%DATADIR%%/matrix/aa/BLOSUM40
+%%DATADIR%%/matrix/aa/BLOSUM45
+%%DATADIR%%/matrix/aa/BLOSUM50
+%%DATADIR%%/matrix/aa/BLOSUM55
+%%DATADIR%%/matrix/aa/BLOSUM60
+%%DATADIR%%/matrix/aa/BLOSUM62
+%%DATADIR%%/matrix/aa/BLOSUM65
+%%DATADIR%%/matrix/aa/BLOSUM70
+%%DATADIR%%/matrix/aa/BLOSUM75
+%%DATADIR%%/matrix/aa/BLOSUM80
+%%DATADIR%%/matrix/aa/BLOSUM85
+%%DATADIR%%/matrix/aa/BLOSUM90
+%%DATADIR%%/matrix/aa/BLOSUMN
+%%DATADIR%%/matrix/aa/blosum100
+%%DATADIR%%/matrix/aa/blosum30
+%%DATADIR%%/matrix/aa/blosum35
+%%DATADIR%%/matrix/aa/blosum40
+%%DATADIR%%/matrix/aa/blosum45
+%%DATADIR%%/matrix/aa/blosum50
+%%DATADIR%%/matrix/aa/blosum55
+%%DATADIR%%/matrix/aa/blosum60
+%%DATADIR%%/matrix/aa/blosumn
+%%DATADIR%%/matrix/aa/blosum62
+%%DATADIR%%/matrix/aa/blosum65
+%%DATADIR%%/matrix/aa/blosum70
+%%DATADIR%%/matrix/aa/blosum75
+%%DATADIR%%/matrix/aa/blosum80
+%%DATADIR%%/matrix/aa/blosum85
+%%DATADIR%%/matrix/aa/DAYHOFF
+%%DATADIR%%/matrix/aa/GONNET
+%%DATADIR%%/matrix/aa/IDENTITY
+%%DATADIR%%/matrix/aa/MATCH
+%%DATADIR%%/matrix/aa/PAM10
+%%DATADIR%%/matrix/aa/NUC.4.2
+%%DATADIR%%/matrix/aa/NUC.4.4
+%%DATADIR%%/matrix/aa/PAM100
+%%DATADIR%%/matrix/aa/PAM110
+%%DATADIR%%/matrix/aa/PAM120
+%%DATADIR%%/matrix/aa/PAM130
+%%DATADIR%%/matrix/aa/PAM120.cdi
+%%DATADIR%%/matrix/aa/PAM140
+%%DATADIR%%/matrix/aa/PAM150
+%%DATADIR%%/matrix/aa/PAM160
+%%DATADIR%%/matrix/aa/PAM170
+%%DATADIR%%/matrix/aa/PAM160.cdi
+%%DATADIR%%/matrix/aa/PAM180
+%%DATADIR%%/matrix/aa/PAM190
+%%DATADIR%%/matrix/aa/PAM20
+%%DATADIR%%/matrix/aa/PAM200
+%%DATADIR%%/matrix/aa/PAM200.cdi
+%%DATADIR%%/matrix/aa/PAM210
+%%DATADIR%%/matrix/aa/PAM220
+%%DATADIR%%/matrix/aa/PAM230
+%%DATADIR%%/matrix/aa/PAM240
+%%DATADIR%%/matrix/aa/PAM250
+%%DATADIR%%/matrix/aa/PAM250.cdi
+%%DATADIR%%/matrix/aa/PAM260
+%%DATADIR%%/matrix/aa/PAM270
+%%DATADIR%%/matrix/aa/PAM280
+%%DATADIR%%/matrix/aa/PAM290
+%%DATADIR%%/matrix/aa/PAM30
+%%DATADIR%%/matrix/aa/PAM300
+%%DATADIR%%/matrix/aa/PAM310
+%%DATADIR%%/matrix/aa/PAM320
+%%DATADIR%%/matrix/aa/PAM330
+%%DATADIR%%/matrix/aa/PAM340
+%%DATADIR%%/matrix/aa/PAM350
+%%DATADIR%%/matrix/aa/PAM360
+%%DATADIR%%/matrix/aa/PAM370
+%%DATADIR%%/matrix/aa/PAM380
+%%DATADIR%%/matrix/aa/PAM390
+%%DATADIR%%/matrix/aa/PAM40
+%%DATADIR%%/matrix/aa/PAM40.cdi
+%%DATADIR%%/matrix/aa/PAM400
+%%DATADIR%%/matrix/aa/PAM410
+%%DATADIR%%/matrix/aa/PAM420
+%%DATADIR%%/matrix/aa/PAM430
+%%DATADIR%%/matrix/aa/PAM440
+%%DATADIR%%/matrix/aa/PAM450
+%%DATADIR%%/matrix/aa/PAM460
+%%DATADIR%%/matrix/aa/PAM470
+%%DATADIR%%/matrix/aa/PAM480
+%%DATADIR%%/matrix/aa/PAM490
+%%DATADIR%%/matrix/aa/PAM50
+%%DATADIR%%/matrix/aa/PAM500
+%%DATADIR%%/matrix/aa/PAM60
+%%DATADIR%%/matrix/aa/PAM70
+%%DATADIR%%/matrix/aa/PAM80
+%%DATADIR%%/matrix/aa/PAM80.cdi
+%%DATADIR%%/matrix/aa/PAM90
+%%DATADIR%%/matrix/aa/blosum90
+%%DATADIR%%/matrix/aa/pam120.cdi
+%%DATADIR%%/matrix/aa/pam160.cdi
+%%DATADIR%%/matrix/aa/dayhoff
+%%DATADIR%%/matrix/aa/gonnet
+%%DATADIR%%/matrix/aa/identity
+%%DATADIR%%/matrix/aa/match
+%%DATADIR%%/matrix/aa/pam10
+%%DATADIR%%/matrix/aa/pam100
+%%DATADIR%%/matrix/aa/pam110
+%%DATADIR%%/matrix/aa/pam120
+%%DATADIR%%/matrix/aa/pam130
+%%DATADIR%%/matrix/aa/pam140
+%%DATADIR%%/matrix/aa/pam150
+%%DATADIR%%/matrix/aa/pam160
+%%DATADIR%%/matrix/aa/pam170
+%%DATADIR%%/matrix/aa/pam180
+%%DATADIR%%/matrix/aa/pam190
+%%DATADIR%%/matrix/aa/pam20
+%%DATADIR%%/matrix/aa/pam200
+%%DATADIR%%/matrix/aa/pam250.cdi
+%%DATADIR%%/matrix/aa/pam210
+%%DATADIR%%/matrix/aa/pam220
+%%DATADIR%%/matrix/aa/pam230
+%%DATADIR%%/matrix/aa/pam240
+%%DATADIR%%/matrix/aa/pam250
+%%DATADIR%%/matrix/aa/pam40.cdi
+%%DATADIR%%/matrix/aa/pam260
+%%DATADIR%%/matrix/aa/pam270
+%%DATADIR%%/matrix/aa/pam280
+%%DATADIR%%/matrix/aa/pam290
+%%DATADIR%%/matrix/aa/pam30
+%%DATADIR%%/matrix/aa/pam300
+%%DATADIR%%/matrix/aa/pam310
+%%DATADIR%%/matrix/aa/pam320
+%%DATADIR%%/matrix/aa/pam330
+%%DATADIR%%/matrix/aa/pam340
+%%DATADIR%%/matrix/aa/pam350
+%%DATADIR%%/matrix/aa/pam360
+%%DATADIR%%/matrix/aa/pam370
+%%DATADIR%%/matrix/aa/pam380
+%%DATADIR%%/matrix/aa/pam390
+%%DATADIR%%/matrix/aa/pam40
+%%DATADIR%%/matrix/aa/pam80.cdi
+%%DATADIR%%/matrix/aa/pam400
+%%DATADIR%%/matrix/aa/pam410
+%%DATADIR%%/matrix/aa/pam420
+%%DATADIR%%/matrix/aa/pam430
+%%DATADIR%%/matrix/aa/pam440
+%%DATADIR%%/matrix/aa/pam450
+%%DATADIR%%/matrix/aa/pam460
+%%DATADIR%%/matrix/aa/pam470
+%%DATADIR%%/matrix/aa/pam480
+%%DATADIR%%/matrix/aa/pam490
+%%DATADIR%%/matrix/aa/pam50
+%%DATADIR%%/matrix/aa/pam500
+%%DATADIR%%/matrix/aa/pam60
+%%DATADIR%%/matrix/aa/pam70
+%%DATADIR%%/matrix/aa/pam80
+%%DATADIR%%/matrix/aa/pam90
+%%DATADIR%%/matrix/aa/pam200.cdi
+%%DATADIR%%/matrix/aa/PHAT_T70_B66
+%%DATADIR%%/matrix/aa/PHAT_T75_B73
+%%DATADIR%%/matrix/aa/PHAT_T80_B78
+%%DATADIR%%/matrix/aa/PHAT_T85_B82
+%%DATADIR%%/matrix/aa/phat_t70_b66
+%%DATADIR%%/matrix/aa/phat_t75_b73
+%%DATADIR%%/matrix/aa/phat_t80_b78
+%%DATADIR%%/matrix/aa/phat_t85_b82
+%%DATADIR%%/matrix/aa/nuc.4.2
+%%DATADIR%%/matrix/aa/BLOSUM100
+%%DATADIR%%/matrix/nt/PUPY.4.4
+%%DATADIR%%/matrix/nt/IDENTITY.4.2
+%%DATADIR%%/matrix/nt/IDENTITY.4.4
+%%DATADIR%%/matrix/nt/identity.4.2
+%%DATADIR%%/matrix/nt/pupy.4.2
+%%DATADIR%%/matrix/nt/pupy.4.4
+%%DATADIR%%/matrix/nt/PUPY.4.2
+%%DATADIR%%/matrix/nt/identity.4.4
+%%DATADIR%%/matrix/README
+%%DATADIR%%/filter/seg
+%%DATADIR%%/filter/seg+xnu
+%%DATADIR%%/filter/xnu+seg
+%%DATADIR%%/filter/nseg
+%%DATADIR%%/filter/dust
+%%DATADIR%%/filter/nmerge
+%%DATADIR%%/filter/xnu
+%%DATADIR%%/filter/pmerge
+%%DATADIR%%/filter/pseg
+%%DATADIR%%/filter/README
+%%DATADIR%%/sysblast.sample
+@dirrm %%DATADIR%%/matrix/aa
+@dirrm %%DATADIR%%/matrix/nt
+@dirrm %%DATADIR%%/matrix
+@dirrm %%DATADIR%%/filter
+@dirrm %%DATADIR%%