Initial import of hmmer version 2.0.

Profile hidden Markov models for biological sequence analysis.

PR:		7120
Submitted by:	Matthew Jason Euclid Barnhart <barnhart@sequencer.wustl.edu>

6 files changed, 86 insertions, 0 deletions

diff --git a/biology/hmmer/Makefile b/biology/hmmer/Makefile
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+++ b/biology/hmmer/Makefile
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+# New ports collection Makefile for: hmmer
+# Version required:	2.0
+# Date created:		June 29 1998
+# Whom:			barnhart@genetics.wustl.edu
+#
+# $Id$
+#
+
+DISTNAME=	hmmer-2.0
+CATEGORIES=	biology
+MASTER_SITES=	ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/
+EXTRACT_SUFX=	.tar.Z
+
+MAINTAINER=	barnhart@genetics.wustl.edu
+
+BUILD_DEPENDS=	perl:${PORTSDIR}/lang/perl5
+
+MAN1=		hmmalign.1 hmmbuild.1 hmmcalibrate.1 hmmconvert.1 hmmemit.1 hmmer.1 hmmpfam.1 hmmsearch.1
+
+WRKSRC=		${WRKDIR}/build/${DISTNAME}
+
+post-build:
+	@ strip ${WRKSRC}/binaries/*
+	@ make test
+
+test:
+	@(cd ${WRKSRC}; make test)
+
+post-install:
+.if !defined(NOPORTDOCS)
+	${MKDIR} ${PREFIX}/share/doc/hmmer
+	${INSTALL_MAN} ${WRKSRC}/Userguide/Userguide.ps ${PREFIX}/share/doc/hmmer
+.endif
+	@ ${CAT} ${PKGDIR}/MESSAGE
+
+.include <bsd.port.mk>
diff --git a/biology/hmmer/distinfo b/biology/hmmer/distinfo
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+++ b/biology/hmmer/distinfo
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+MD5 (hmmer-2.0.tar.Z) = 7e993a3883046840f0672ea004bc268b
diff --git a/biology/hmmer/pkg-comment b/biology/hmmer/pkg-comment
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+++ b/biology/hmmer/pkg-comment
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+Profile hidden Markov models for biological sequence analysis.
diff --git a/biology/hmmer/pkg-descr b/biology/hmmer/pkg-descr
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+++ b/biology/hmmer/pkg-descr
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+HMMER is an implementation of profile HMM methods for sensitive database 
+searches using multiple sequence alignments as queries.
+
+Basically, you give HMMER a multiple sequence alignment as input; it builds 
+a statistical model called a "hidden Markov model" which you can then use as 
+a query into a sequence database to find (and/or align) additional 
+homologues of the sequence family.
+
+Hmmer is developed by Sean Eddy at Washington University School of Medicine.
+More information is available at http://hmmer.wustl.edu/
diff --git a/biology/hmmer/pkg-message b/biology/hmmer/pkg-message
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+++ b/biology/hmmer/pkg-message
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+*********************************************************
+
+Note on environment variables:
+
+   HMMER reads three environment variables:
+      HMMERDB  - directory location of HMM databases (e.g. PFAM)
+      BLASTDB  - directory location of FASTA-formatted sequence databases
+      BLASTMAT - directory location of PAM scoring matrices
+
+   If you have installed BLAST, you probably already have these 
+   environment variables set in system-wide or user-specific
+   .cshrc files. They are optional. If they are set up, you
+   can simplify command lines to:
+      > hmmpfam pfam my.query
+      > hmmsearch my.hmm swiss35
+   instead of
+      > hmmpfam   /some/long/path/to/databases/pfam my.query
+      > hmmsearch my.hmm /some/long/path/to/databases/swiss35
+
+Please see the website http://hmmer.wustl.edu/ for more information.
+
+*********************************************************
diff --git a/biology/hmmer/pkg-plist b/biology/hmmer/pkg-plist
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index 000000000000..016506e3ef22
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+++ b/biology/hmmer/pkg-plist
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+bin/hmmalign
+bin/hmmbuild
+bin/hmmcalibrate
+bin/hmmconvert
+bin/hmmemit
+bin/hmmpfam
+bin/hmmsearch
+man/man1/hmmalign.1.gz
+man/man1/hmmbuild.1.gz
+man/man1/hmmcalibrate.1.gz
+man/man1/hmmconvert.1.gz
+man/man1/hmmemit.1.gz
+man/man1/hmmer.1.gz
+man/man1/hmmpfam.1.gz
+man/man1/hmmsearch.1.gz
+share/doc/hmmer/Userguide.ps