kpriv/pkgsrc
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity
pkgsrc/biology/glimmer/PLIST

22 lines
477 B
Text
Raw Normal View History

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
@comment $NetBSD: PLIST,v 1.2 2003/10/07 18:20:15 jschauma 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
bin/adjust
bin/anomaly
bin/build-icm
bin/check
bin/codon-usage
bin/compare-lists
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
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
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
Reference in a new issue Copy permalink