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.

5 files changed, 74 insertions, 0 deletions

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);\