FreshPorts -- The Place For Ports If you buy from Amazon USA, please support us by using this link.
Follow us
Blog
Twitter

I am looking for an LTO tape library. Do you have one to spare?
Port details
gmap 2006.04.21_1 biology on this many watch lists=0 search for ports that depend on this port
Genomic Mapping and Alignment Program for mRNA and EST Sequences
Maintained by: rpz@cse.wustl.edu search for ports maintained by this maintainer
Port Added: 29 Sep 2006 04:09:50
License: not specified in port


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
SVNWeb : Main Web Site : Distfiles Availability : PortsMon

NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Required To Build:
  1. devel/gmake
  2. lang/perl5.16
Required To Run:
  1. lang/perl5.16
There are no ports dependent upon this port

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


Configuration Options
     No options to configure

Master Sites:
  1. http://distcache.FreeBSD.org/ports-distfiles/
  2. http://research-pub.gene.com/gmap/src/

Number of commits found: 7

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
05 Sep 2014 09:25:46
Original commit files touched by this commit  2006.04.21_1
Revision:367328
antoine search for other commits by this committer
Fix MASTER_SITES

Submitted by:	tijl@
10 Dec 2013 17:21:46
Original commit files touched by this commit  2006.04.21_1
Revision:336070
bapt search for other commits by this committer
Support stage
Convert USE_GMAKE to USES=gmake
Add dependency on perl which the port need and was getting by chance
bump portrevision, dependencies has changed
20 Sep 2013 15:55:44
Original commit files touched by this commit  2006.04.21
Revision:327709
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
12 Dec 2010 08:10:05
Original commit files touched by this commit  2006.04.21
pgollucci search for other commits by this committer
- fix fetch: wget is not required for fetching

Reported by:    QAT
21 Aug 2008 06:18:49
Original commit files touched by this commit  2006.04.21
rafan search for other commits by this committer
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
(Only the first 15 lines of the commit message are shown above View all of this commit message)
16 Apr 2007 21:18:53
Original commit files touched by this commit  2006.04.21
edwin search for other commits by this committer
[patch] cleanup non-supported FreeBSD versions

PR:             ports/111727
Submitted by:   Edwin Groothuis <edwin@mavetju.org>
Approved by:    Bob Zimmermann <rpz@cse.wustl.edu>
29 Sep 2006 04:05:55
Original commit files touched by this commit  2006.04.21
clsung search for other commits by this committer
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>

Number of commits found: 7

Login
User Login
Create account

Servers and bandwidth provided by
New York Internet, SuperNews, and RootBSD

This site
What is FreshPorts?
About the authors
FAQ
How big is it?
The latest upgrade!
Privacy
Forums
Blog
Contact

Search
Enter Keywords:
 
more...

Latest Vulnerabilities
asterisk11Sep 18
squidSep 18
squid33Sep 18
dbusSep 17
nginxSep 16
nginx-develSep 16
phpmyadminSep 13
ossec-hids-clientSep 11
ossec-hids-localSep 11
ossec-hids-serverSep 11
chromiumSep 09
trafficserverSep 05
apache22*Sep 03
apache22-event-mpm*Sep 03
apache22-itk-mpm*Sep 03

8 vulnerabilities affecting 19 ports have been reported in the past 14 days

* - modified, not new

All vulnerabilities


Ports
Home
Categories
Deleted ports
Sanity Test Failures
Newsfeeds


Statistics
Graphs
NEW Graphs (Javascript)
Traffic

Calculated hourly:
Port count 24063
Broken 118
Deprecated 54
Ignore 370
Forbidden 4
Restricted 203
No CDROM 94
Vulnerable 21
Expired 6
Set to expire 49
Interactive 0
new 24 hours 6
new 48 hours7
new 7 days36
new fortnight70
new month232

Servers and bandwidth provided by
New York Internet, SuperNews, and RootBSD
Valid HTML, CSS, and RSS.
Copyright © 2000-2014 Dan Langille. All rights reserved.