diff options
| -rw-r--r-- | biology/glimmer/DESCR | 6 | ||||
| -rw-r--r-- | biology/glimmer/Makefile | 29 | ||||
| -rw-r--r-- | biology/glimmer/PLIST | 21 | ||||
| -rw-r--r-- | biology/glimmer/distinfo | 5 | ||||
| -rw-r--r-- | biology/glimmer/patches/patch-aa | 17 |
5 files changed, 78 insertions, 0 deletions
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 |