gmap 2006.04.21 biology =0

A Genomic Mapping and Alignment Program for mRNA and EST Sequences
Maintained by: rpz@cse.wustl.edu
Port Added: 29 Sep 2006 04:09:50
License: not specified in port

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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

CVSWeb : Sources : Main Web Site : Distfiles Availability : PortsMon

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NOTE: FreshPorts displays only required dependencies information. Optional dependencies are not covered.
Required To Build: devel/gmake
There are no ports dependent upon this port

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To install the port: cd /usr/ports/biology/gmap/ && make install clean
To add the package: pkg_add -r gmap

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Configuration Options

     No options to configure

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Master Sites:

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

ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/

- fix fetch: wget is not required for fetching

Reported by:    QAT

Update CONFIGURE_ARGS for how we pass CONFIGURE_TARGET to configure script.
Specifically, newer autoconf (> 2.13) has different semantic of the
configure target. In short, one should use --build=CONFIGURE_TARGET
instead of CONFIGURE_TARGET directly. Otherwise, you will get a warning
and the old semantic may be removed in later autoconf releases.

To workaround this issue, many ports hack the CONFIGURE_TARGET variable
so that it contains the ``--build='' prefix.

To solve this issue, under the fact that some ports still have
configure script generated by the old autoconf, we use runtime detection
in the do-configure target so that the proper argument can be used.

Changes to Mk/*:
 - Add runtime detection magic in bsd.port.mk

[patch] cleanup non-supported FreeBSD versions

PR:             ports/111727
Submitted by:   Edwin Groothuis <edwin@mavetju.org>
Approved by:    Bob Zimmermann <rpz@cse.wustl.edu>

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>

12 vulnerabilities affecting 17 ports have been reported in the past 14 days

^* - modified, not new

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