Bug 103651

Summary: new port: biology/gmap, a standalone program for mapping and aligning cDNA sequences to a genome
Product: Ports & Packages Reporter: Bob Zimmermann <rpz>
Component: Individual Port(s)Assignee: Cheng-Lung Sung <clsung>
Status: Closed FIXED    
Severity: Affects Only Me    
Priority: Normal    
Version: Latest   
Hardware: Any   
OS: Any   
Attachments:
Description Flags
file.shar none

Description Bob Zimmermann 2006-09-25 23:00:34 UTC 
A standalone program for mapping and aligning cDNA sequences to a
genome. The program maps and aligns a single sequence with minimal
startup time and memory requirements, and provides fast batch
processing of large sequence sets. The program generates accurate
gene structures, even in the presence of substantial polymorphisms
and sequence errors, without using probabilistic splice site models.
Methodology underlying the program includes a minimal sampling
strategy for genomic mapping, oligomer chaining for approximate
alignment, sandwich DP for splice site detection, and microexon
identification with statistical significance testing.

WWW: http://www.gene.com/share/gmap

Fix: (port add, not a bug)


port shar archive:

How-To-Repeat: (port add, not a bug)
Comment 1 Cheng-Lung Sung freebsd_committer freebsd_triage 2006-09-27 02:32:53 UTC 
Responsible Changed
From-To: freebsd-ports-bugs->clsung

I'll take it.
Comment 2 Cheng-Lung Sung freebsd_committer freebsd_triage 2006-09-29 02:07:02 UTC 
This port does not build on 4.x

http://tb.newzilla.org/errors/4-perl5005/gmap-2006.04.21.log

Can you fix it?

On Mon, Sep 25, 2006 at 04:51:21PM -0500, Bob Zimmermann wrote:
>=20
--=20
Cheng-Lung Sung - clsung@
Comment 3 dfilter service freebsd_committer freebsd_triage 2006-09-29 05:06:02 UTC 
clsung      2006-09-29 04:05:55 UTC

  FreeBSD ports repository

  Modified files:
    biology              Makefile 
  Added files:
    biology/gmap         Makefile distinfo pkg-descr pkg-plist 
    biology/gmap/files   extra-patch-src-genome.c 
                         extra-patch-src-indexdb.c patch-configure 
  Log:
  Add gmap 2006.04.21, a Genomic Mapping and Alignment Program for mRNA
  and EST Sequences.
  
  PR:             ports/103651
  Submitted by:   Bob Zimmermann <rpz at cse.wustl.edu>
  
  Revision  Changes    Path
  1.88      +1 -0      ports/biology/Makefile
  1.1       +32 -0     ports/biology/gmap/Makefile (new)
  1.1       +3 -0      ports/biology/gmap/distinfo (new)
  1.1       +17 -0     ports/biology/gmap/files/extra-patch-src-genome.c (new)
  1.1       +17 -0     ports/biology/gmap/files/extra-patch-src-indexdb.c (new)
  1.1       +11 -0     ports/biology/gmap/files/patch-configure (new)
  1.1       +12 -0     ports/biology/gmap/pkg-descr (new)
  1.1       +12 -0     ports/biology/gmap/pkg-plist (new)
_______________________________________________
cvs-all@freebsd.org mailing list
http://lists.freebsd.org/mailman/listinfo/cvs-all
To unsubscribe, send any mail to "cvs-all-unsubscribe@freebsd.org"
Comment 4 Cheng-Lung Sung freebsd_committer freebsd_triage 2006-09-29 05:09:38 UTC 
State Changed
From-To: open->closed

New port added. Thank you.