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>
This commit is contained in:
Steve Price 1998-07-12 23:30:04 +00:00
parent 70bef47e58
commit 91f5c278fe
Notes: svn2git 2021-03-31 03:12:20 +00:00
svn path=/head/; revision=11871
6 changed files with 86 additions and 0 deletions

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biology/hmmer/Makefile Normal file
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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>

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MD5 (hmmer-2.0.tar.Z) = 7e993a3883046840f0672ea004bc268b

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Profile hidden Markov models for biological sequence analysis.

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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/

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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.
*********************************************************

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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