diff options
| -rw-r--r-- | biology/hmmer/Makefile | 36 | ||||
| -rw-r--r-- | biology/hmmer/distinfo | 1 | ||||
| -rw-r--r-- | biology/hmmer/pkg-comment | 1 | ||||
| -rw-r--r-- | biology/hmmer/pkg-descr | 10 | ||||
| -rw-r--r-- | biology/hmmer/pkg-message | 22 | ||||
| -rw-r--r-- | biology/hmmer/pkg-plist | 16 |
6 files changed, 86 insertions, 0 deletions
diff --git a/biology/hmmer/Makefile b/biology/hmmer/Makefile new file mode 100644 index 000000000000..f64e60ae355a --- /dev/null +++ b/biology/hmmer/Makefile @@ -0,0 +1,36 @@ +# 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 new file mode 100644 index 000000000000..c9d8219fb787 --- /dev/null +++ b/biology/hmmer/distinfo @@ -0,0 +1 @@ +MD5 (hmmer-2.0.tar.Z) = 7e993a3883046840f0672ea004bc268b diff --git a/biology/hmmer/pkg-comment b/biology/hmmer/pkg-comment new file mode 100644 index 000000000000..7859aefe98e9 --- /dev/null +++ b/biology/hmmer/pkg-comment @@ -0,0 +1 @@ +Profile hidden Markov models for biological sequence analysis. diff --git a/biology/hmmer/pkg-descr b/biology/hmmer/pkg-descr new file mode 100644 index 000000000000..869b22f5c3e6 --- /dev/null +++ b/biology/hmmer/pkg-descr @@ -0,0 +1,10 @@ +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 new file mode 100644 index 000000000000..dbfd059121b1 --- /dev/null +++ b/biology/hmmer/pkg-message @@ -0,0 +1,22 @@ +********************************************************* + +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 new file mode 100644 index 000000000000..016506e3ef22 --- /dev/null +++ b/biology/hmmer/pkg-plist @@ -0,0 +1,16 @@ +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 |