[pkgsrc/trunk]: pkgsrc/biology/glimmer Initial import of glimmer, one of the ...

[jschauma <jschauma%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/65fea36d0f15
branches:  trunk
changeset: 462300:65fea36d0f15
user:      jschauma <jschauma%pkgsrc.org@localhost>
date:      Tue Sep 30 02:11:06 2003 +0000

description:
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.

diffstat:

 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(+), 0 deletions(-)

diffs (98 lines):

diff -r 85b1a9013ebf -r 65fea36d0f15 biology/glimmer/DESCR
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/glimmer/DESCR     Tue Sep 30 02:11:06 2003 +0000
@@ -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 -r 85b1a9013ebf -r 65fea36d0f15 biology/glimmer/Makefile
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/glimmer/Makefile  Tue Sep 30 02:11:06 2003 +0000
@@ -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@localhost
+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 -r 85b1a9013ebf -r 65fea36d0f15 biology/glimmer/PLIST
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/glimmer/PLIST     Tue Sep 30 02:11:06 2003 +0000
@@ -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 -r 85b1a9013ebf -r 65fea36d0f15 biology/glimmer/distinfo
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/glimmer/distinfo  Tue Sep 30 02:11:06 2003 +0000
@@ -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 -r 85b1a9013ebf -r 65fea36d0f15 biology/glimmer/patches/patch-aa
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/glimmer/patches/patch-aa  Tue Sep 30 02:11:06 2003 +0000
@@ -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