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pkgsrc/biology/glimmer/Makefile

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Remove USE_BUILDLINK3 and NO_BUILDLINK; these are no longer used.
2005-04-11 23:44:48 +02:00
# $NetBSD: Makefile,v 1.6 2005/04/11 21:45:00 tv Exp $
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.
2003-09-30 04:11:06 +02:00
#
Update to glimmer-2.13, thanks to cngo@nmsu.edu. CHANGELOG, 12 October 2003 add -X option to glimmer2, to allow orfs extending off ends of sequence to be scored. Also fix bug affecting -p and -o options when user chose zero overlap.
2004-08-19 18:47:01 +02:00
DISTNAME= glimmer213
PKGNAME= glimmer-2.13
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.
2003-09-30 04:11:06 +02:00
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
Update to glimmer-2.13, thanks to cngo@nmsu.edu. CHANGELOG, 12 October 2003 add -X option to glimmer2, to allow orfs extending off ends of sequence to be scored. Also fix bug affecting -p and -o options when user chose zero overlap.
2004-08-19 18:47:01 +02:00
WRKSRC= ${WRKDIR}/glimmer2.13
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.
2003-09-30 04:11:06 +02:00
do-install:
Apply patches from Tyler Retzlaff in PR pkg/23083 to make this behave with gcc3. While here, update to version 2.12 (previous version was erraneously named 2.1, when it should have been 2.10) which is the only distfile available on the ftp site. Changelog seems to say: - Fix bug on long-orfs.cc to avoid occasional array out-of-bounds error (detected on Mac OS X).
2003-10-07 20:20:15 +02:00
.for PROGRAM in adjust anomaly build-icm check codon-usage compare-lists \
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.
2003-09-30 04:11:06 +02:00
generate get-len get-putative glimmer2 long-orfs
${INSTALL_PROGRAM} ${WRKSRC}/${PROGRAM} ${PREFIX}/bin
.endfor
Apply patches from Tyler Retzlaff in PR pkg/23083 to make this behave with gcc3. While here, update to version 2.12 (previous version was erraneously named 2.1, when it should have been 2.10) which is the only distfile available on the ftp site. Changelog seems to say: - Fix bug on long-orfs.cc to avoid occasional array out-of-bounds error (detected on Mac OS X).
2003-10-07 20:20:15 +02:00
# ``extract'' is also in the csound package, so rename to avoid conflict
${INSTALL_PROGRAM} ${WRKSRC}/extract ${PREFIX}/bin/glextract
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.
2003-09-30 04:11:06 +02:00
${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"
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