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authorSteve Price <steve@FreeBSD.org>1998-07-12 23:30:04 +0000
committerSteve Price <steve@FreeBSD.org>1998-07-12 23:30:04 +0000
commit91f5c278fe07c962bdfa655fbe8b8bbae7c2e49e (patch)
tree6724ceb40dbf396309d33eb1a55fc256f43ca250
parent70bef47e5818f970b18cc7768989e0f3a98ab07d (diff)
downloadports-91f5c278fe07c962bdfa655fbe8b8bbae7c2e49e.tar.gz
ports-91f5c278fe07c962bdfa655fbe8b8bbae7c2e49e.zip
Notes
-rw-r--r--biology/hmmer/Makefile36
-rw-r--r--biology/hmmer/distinfo1
-rw-r--r--biology/hmmer/pkg-comment1
-rw-r--r--biology/hmmer/pkg-descr10
-rw-r--r--biology/hmmer/pkg-message22
-rw-r--r--biology/hmmer/pkg-plist16
6 files changed, 86 insertions, 0 deletions
diff --git a/biology/hmmer/Makefile b/biology/hmmer/Makefile
new file mode 100644
index 000000000000..f64e60ae355a
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+++ 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