From b92c4d6b4bb77d45bc347dc57154865f7c61920e Mon Sep 17 00:00:00 2001
From: jschauma <jschauma@pkgsrc.org>
Date: Tue, 30 Sep 2003 02:11:06 +0000
Subject: Initial import of glimmer, one of the many packages provided by brook
 at biology dot nmsu dot edu and his team at NMSU.

Glimmer (Gene Locator and Interpolated Markov Modeler) is a system for finding
genes in microbial DNA, especially the genomes of bacteria and archaea.
Glimmer uses interpolated Markov models (IMMs) to identify the coding regions
and  distinguish them from noncoding DNA. The IMM approach uses a combination
of Markov models from 1st through 8th-order, weighting each model according to
its predictive power.
---
 biology/glimmer/DESCR            |  6 ++++++
 biology/glimmer/Makefile         | 29 +++++++++++++++++++++++++++++
 biology/glimmer/PLIST            | 21 +++++++++++++++++++++
 biology/glimmer/distinfo         |  5 +++++
 biology/glimmer/patches/patch-aa | 17 +++++++++++++++++
 5 files changed, 78 insertions(+)
 create mode 100644 biology/glimmer/DESCR
 create mode 100644 biology/glimmer/Makefile
 create mode 100644 biology/glimmer/PLIST
 create mode 100644 biology/glimmer/distinfo
 create mode 100644 biology/glimmer/patches/patch-aa

(limited to 'biology/glimmer')

diff --git a/biology/glimmer/DESCR b/biology/glimmer/DESCR
new file mode 100644
index 00000000000..f21dd550ce1
--- /dev/null
+++ b/biology/glimmer/DESCR
@@ -0,0 +1,6 @@
+Glimmer (Gene Locator and Interpolated Markov Modeler) is a system for finding
+genes in microbial DNA, especially the genomes of bacteria and archaea.
+Glimmer uses interpolated Markov models (IMMs) to identify the coding regions
+and  distinguish them from noncoding DNA. The IMM approach uses a combination
+of Markov models from 1st through 8th-order, weighting each model according to
+its predictive power. 
diff --git a/biology/glimmer/Makefile b/biology/glimmer/Makefile
new file mode 100644
index 00000000000..5b9c3dbcf3f
--- /dev/null
+++ b/biology/glimmer/Makefile
@@ -0,0 +1,29 @@
+# $NetBSD: Makefile,v 1.1.1.1 2003/09/30 02:11:06 jschauma Exp $
+#
+
+DISTNAME=		glimmer21
+PKGNAME=		glimmer-2.1
+WRKSRC=                 ${WRKDIR}/glimmer2.10
+CATEGORIES=		biology
+MASTER_SITES=		ftp://ftp.tigr.org/pub/software/Glimmer/
+
+MAINTAINER=		hdp@cs.nmsu.edu
+HOMEPAGE=		ftp://ftp.tigr.org/pub/software/Glimmer/
+COMMENT=		System for finding genes in microbial DNA
+
+USE_BUILDLINK2=		yes
+
+do-install:
+.for PROGRAM in adjust anomaly build-icm check codon-usage compare-lists extract \
+	generate get-len get-putative glimmer2 long-orfs
+	${INSTALL_PROGRAM} ${WRKSRC}/${PROGRAM} ${PREFIX}/bin
+.endfor
+	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/glimmer
+	${CP} ${WRKSRC}/README ${WRKSRC}/run-glimmer2.readme
+.for DOC in run-glimmer2.readme build-icm.readme extract.readme glimmer2.readme long-orfs.readme
+	${INSTALL_DATA} ${WRKSRC}/${DOC} ${PREFIX}/share/doc/glimmer
+.endfor
+	${INSTALL_DATA_DIR} ${PREFIX}/share/glimmer
+	${INSTALL_SCRIPT} ${WRKSRC}/run-glimmer2 ${PREFIX}/share/glimmer
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/biology/glimmer/PLIST b/biology/glimmer/PLIST
new file mode 100644
index 00000000000..f4fde8226a4
--- /dev/null
+++ b/biology/glimmer/PLIST
@@ -0,0 +1,21 @@
+@comment $NetBSD: PLIST,v 1.1.1.1 2003/09/30 02:11:06 jschauma Exp $
+bin/adjust
+bin/anomaly
+bin/build-icm
+bin/check
+bin/codon-usage
+bin/compare-lists
+bin/extract
+bin/generate
+bin/get-len
+bin/get-putative
+bin/glimmer2
+bin/long-orfs
+share/doc/glimmer/build-icm.readme
+share/doc/glimmer/extract.readme
+share/doc/glimmer/glimmer2.readme
+share/doc/glimmer/long-orfs.readme
+share/doc/glimmer/run-glimmer2.readme
+share/glimmer/run-glimmer2
+@dirrm share/glimmer
+@dirrm share/doc/glimmer
diff --git a/biology/glimmer/distinfo b/biology/glimmer/distinfo
new file mode 100644
index 00000000000..139ebb80861
--- /dev/null
+++ b/biology/glimmer/distinfo
@@ -0,0 +1,5 @@
+$NetBSD: distinfo,v 1.1.1.1 2003/09/30 02:11:06 jschauma Exp $
+
+SHA1 (glimmer21.tar.gz) = 676bf2150389b4eb817ef2db7c646a332151eaf7
+Size (glimmer21.tar.gz) = 79091 bytes
+SHA1 (patch-aa) = ceb45f887c32e91bd96b9d2c8dae39c9cc6fc658
diff --git a/biology/glimmer/patches/patch-aa b/biology/glimmer/patches/patch-aa
new file mode 100644
index 00000000000..e965db78651
--- /dev/null
+++ b/biology/glimmer/patches/patch-aa
@@ -0,0 +1,17 @@
+$NetBSD: patch-aa,v 1.1.1.1 2003/09/30 02:11:06 jschauma Exp $
+
+--- Makefile.orig	2003-09-29 22:02:13.000000000 -0400
++++ Makefile	2003-09-29 22:02:45.000000000 -0400
+@@ -4,9 +4,9 @@
+ PROJECTDIR = .
+ BINDIR = $(PROJECTDIR)
+ 
+-CC = gcc
+-CPPC = g++
+-CFLAGS = -O3 -g -Wall
++#CC = gcc
++CPPC = ${CXX}
++#CFLAGS = -O3 -g -Wall
+ LDFLAGS = -lm
+ 
+ DEPEND_FILES = *.cc *.c *.h
-- 
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