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Port details
velvet 1.2.10_1 biology on this many watch lists=0 search for ports that depend on this port
Sequence assembler for very short reads
Maintained by: mzaki@m.u-tokyo.ac.jp search for ports maintained by this maintainer
Port Added: 07 Nov 2009 01:24:24
License: not specified in port


Velvet is a de novo genomic assembler specially designed for short read
sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino
and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI).

Citation:

Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
D.R. Zerbino and E. Birney. Genome Research 18: 821-829 (2008)

WWW: http://www.ebi.ac.uk/~zerbino/velvet/
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. lang/python27
  2. devel/gmake
Required To Run:
  1. lang/python27
  2. lang/perl5.16
There are no ports dependent upon this port

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


Configuration Options
===> The following configuration options are available for velvet-1.2.10_1:
     DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings

Master Sites:
  1. http://distcache.FreeBSD.org/ports-distfiles/
  2. http://www.ebi.ac.uk/~zerbino/velvet/

Number of commits found: 13

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
29 Jul 2014 19:11:53
Original commit files touched by this commit  1.2.10_1
Revision:363374
adamw search for other commits by this committer
Convert a bunch of EXTRACT_SUFX=... into USES=tar:...

Approved by:	portmgr (not really, but touches unstaged ports)
20 Jun 2014 12:54:29
Original commit files touched by this commit  1.2.10_1
Revision:358567
rakuco search for other commits by this committer
Fix shebang line in Perl and Python scripts.

PR:		191146
Submitted by:	mzaki@m.u-tokyo.ac.jp (maintainer)
17 Jun 2014 21:39:44
Original commit files touched by this commit  1.2.10
Revision:358183
rakuco search for other commits by this committer
Update to 1.2.10.

PR:		191129
Submitted by:	mzaki@m.u-tokyo.ac.jp (maintainer)
01 Jun 2014 11:33:57
Original commit files touched by this commit  1.1.04
Revision:356099
ohauer search for other commits by this committer
- add stage support
13 Mar 2014 07:41:34
Original commit files touched by this commit  1.1.04
Revision:348042
miwi search for other commits by this committer
- Convert USE_GMAKE to USES
21 Feb 2014 13:35:26
Original commit files touched by this commit  1.1.04
Revision:345397
ehaupt search for other commits by this committer
Remove trailing whitespaces from category biology
10 Feb 2014 13:54:28
Original commit files touched by this commit  1.1.04
Revision:343634
ehaupt search for other commits by this committer
According to the Porter's Handbook (5.12.2.3.) default options must be added to
OPTIONS_DEFINE. This policy has been implemented only recently that's why we
have many ports violating this policy.

This patch adds the default options specified in the Porter's Handbook to
OPTIONS_DEFINE where they are being used. Ports maintained by
gnome@FreeBSD.org, kde@FreeBSD.org and x11@FreeBSD.org have been excluded.

Approved by:    portmgr (bapt)
03 Jan 2014 15:46:52
Original commit files touched by this commit  1.1.04
Revision:338550
adamw search for other commits by this committer
Convert biology to MDOCS and MEXAMPLES
20 Sep 2013 15:55:44
Original commit files touched by this commit  1.1.04
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)
07 Sep 2013 07:44:27
Original commit files touched by this commit  1.1.04
Revision:326575
az search for other commits by this committer
- convert to the new perl5 framework

Approved by:	portmgr (bapt@, blanket)
09 Jun 2011 16:33:21
Original commit files touched by this commit  1.1.04
jlaffaye search for other commits by this committer
Update to 1.1.04

PR:             ports/157527
Submitted by:   Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>
Approved by:    bapt (mentor)
19 Mar 2011 12:38:54
Original commit files touched by this commit  0.7.55
miwi search for other commits by this committer
- Get Rid MD5 support
07 Nov 2009 01:23:59
Original commit files touched by this commit  0.7.55
amdmi3 search for other commits by this committer
Velvet is a de novo genomic assembler specially designed for short read
sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino
and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI).

Citation:

Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
D.R. Zerbino and E. Birney. Genome Research 18: 821-829 (2008)

WWW: http://www.ebi.ac.uk/~zerbino/velvet/

PR:             140147
Submitted by:   Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>

Number of commits found: 13

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