From c3f38745bc10a6e20dd4d99a5222431f6281921c Mon Sep 17 00:00:00 2001
From: jschauma <jschauma>
Date: Fri, 26 Sep 2003 03:52:47 +0000
Subject: Initial import of hmmer,  one of the many packages provided by brook
 at biology dot nmsu dot edu and his team at NMSU.

HMMER is an implementation of profile HMM methods for sensitive database
searches using multiple sequence alignments as queries. HMMER takes
multiple sequence alignement as input and builds statistical model
called "Hidden Markov Model" which can be used as a query into a
sequence database to find and/or align additional homologues of the
sequence family.
---
 biology/hmmer/DESCR            |  6 ++++++
 biology/hmmer/Makefile         | 16 ++++++++++++++++
 biology/hmmer/PLIST            | 20 ++++++++++++++++++++
 biology/hmmer/distinfo         |  5 +++++
 biology/hmmer/patches/patch-aa | 27 +++++++++++++++++++++++++++
 5 files changed, 74 insertions(+)
 create mode 100644 biology/hmmer/DESCR
 create mode 100644 biology/hmmer/Makefile
 create mode 100644 biology/hmmer/PLIST
 create mode 100644 biology/hmmer/distinfo
 create mode 100644 biology/hmmer/patches/patch-aa

(limited to 'biology')

diff --git a/biology/hmmer/DESCR b/biology/hmmer/DESCR
new file mode 100644
index 00000000000..fe451f2ada7
--- /dev/null
+++ b/biology/hmmer/DESCR
@@ -0,0 +1,6 @@
+HMMER is an implementation of profile HMM methods for sensitive database 
+searches using multiple sequence alignments as queries. HMMER takes 
+multiple sequence alignement as input and builds statistical model 
+called "Hidden Markov Model" which can be used as a query into a 
+sequence database to find and/or align additional homologues of the 
+sequence family.
diff --git a/biology/hmmer/Makefile b/biology/hmmer/Makefile
new file mode 100644
index 00000000000..db1c4d7d724
--- /dev/null
+++ b/biology/hmmer/Makefile
@@ -0,0 +1,16 @@
+# $NetBSD: Makefile,v 1.1.1.1 2003/09/26 03:52:47 jschauma Exp $
+#
+
+DISTNAME=		hmmer-2.3.1
+WRKSRC=			${WRKDIR}/hmmer-2.3.1
+CATEGORIES=		biology
+MASTER_SITES=		ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/2.3.1/
+
+MAINTAINER=		hdp@cs.nmsu.edu
+HOMEPAGE=		http://hmmer.wustl.edu
+COMMENT=		Implementation of profile HMM software for protein sequence analysis
+
+USE_BUILDLINK2=		yes
+GNU_CONFIGURE=		yes
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/biology/hmmer/PLIST b/biology/hmmer/PLIST
new file mode 100644
index 00000000000..5dd1779c36a
--- /dev/null
+++ b/biology/hmmer/PLIST
@@ -0,0 +1,20 @@
+@comment $NetBSD: PLIST,v 1.1.1.1 2003/09/26 03:52:47 jschauma Exp $
+bin/hmmalign
+bin/hmmbuild
+bin/hmmcalibrate
+bin/hmmconvert
+bin/hmmemit
+bin/hmmfetch
+bin/hmmindex
+bin/hmmpfam
+bin/hmmsearch
+man/man1/hmmalign.1
+man/man1/hmmbuild.1
+man/man1/hmmcalibrate.1
+man/man1/hmmconvert.1
+man/man1/hmmemit.1
+man/man1/hmmer.1
+man/man1/hmmfetch.1
+man/man1/hmmindex.1
+man/man1/hmmpfam.1
+man/man1/hmmsearch.1
diff --git a/biology/hmmer/distinfo b/biology/hmmer/distinfo
new file mode 100644
index 00000000000..81045d8f3ec
--- /dev/null
+++ b/biology/hmmer/distinfo
@@ -0,0 +1,5 @@
+$NetBSD: distinfo,v 1.1.1.1 2003/09/26 03:52:47 jschauma Exp $
+
+SHA1 (hmmer-2.3.1.tar.gz) = bf6a3ec56c24332d7e66d6ce8865de1d72dce01f
+Size (hmmer-2.3.1.tar.gz) = 1023122 bytes
+SHA1 (patch-aa) = c5aa41137bb339a584948b6dc88317c98b4ff6fd
diff --git a/biology/hmmer/patches/patch-aa b/biology/hmmer/patches/patch-aa
new file mode 100644
index 00000000000..08716d03d06
--- /dev/null
+++ b/biology/hmmer/patches/patch-aa
@@ -0,0 +1,27 @@
+$NetBSD: patch-aa,v 1.1.1.1 2003/09/26 03:52:47 jschauma Exp $
+
+--- Makefile.in.orig	2003-06-13 17:05:13.000000000 -0400
++++ Makefile.in	2003-09-25 23:47:27.000000000 -0400
+@@ -30,11 +30,12 @@
+ exec_prefix = @exec_prefix@
+ BINDIR      = @bindir@
+ MANDIR      = @mandir@
++INSTBIN     = ${BSD_INSTALL_PROGRAM}
+ 
+ # how to install the man pages; 
+ # cp is generally fine, unless you preformat your pages.
+ #
+-INSTMAN   = cp
++INSTMAN   = ${BSD_INSTALL_MAN}
+ MANSUFFIX = 1
+ 
+ # your compiler and compiler flags
+@@ -112,7 +113,7 @@
+ 	mkdir -p ${BINDIR}
+ 	-mkdir -p ${MANDIR}/man${MANSUFFIX}
+ 	for file in $(PROGS) $(PVMPROGS); do\
+-	   cp src/$$file $(BINDIR)/;\
++	   $(INSTBIN) src/$$file $(BINDIR)/;\
+ 	done
+ 	-for file in hmmer $(PROGS); do\
+ 	   $(INSTMAN) documentation/man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
-- 
cgit v1.2.3