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Port details
velvet Sequence assembler for very short reads
1.2.10_2 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port 1.2.10Version of this port present on the latest quarterly branch.
Maintainer: mzaki@m.u-tokyo.ac.jp search for ports maintained by this maintainer
Port Added: 2009-11-07 01:24:24
Last Update: 2018-01-11 18:09:00
SVN Revision: 458761
License: not specified in port
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (23 items)
  1. bin/velvetg
  2. bin/velveth
  3. bin/shuffleSequences_fasta.pl
  4. bin/shuffleSequences_fastq.pl
  5. bin/VelvetOptimiser.pl
  6. bin/asmbly_splitter.pl
  7. bin/snp_view.pl
  8. bin/enlarge_exons.pl
  9. bin/gff2fasta.pl
  10. bin/merge_gtf_exons.pl
  11. bin/velvet-estimate-exp_cov.pl
  12. bin/extractContigReads.pl
  13. bin/fasta2agp.pl
  14. bin/observed-insert-length.pl
  15. bin/pe_read_prepare.0.1.pl
  16. bin/select_paired.pl
  17. bin/show_repeats.pl
  18. bin/AssemblyAssembler1.3.py
  19. lib/perl5/site_perl/VelvetOpt/Assembly.pm
  20. lib/perl5/site_perl/VelvetOpt/Utils.pm
  21. lib/perl5/site_perl/VelvetOpt/gwrap.pm
  22. lib/perl5/site_perl/VelvetOpt/hwrap.pm
  23. @dir lib/perl5/site_perl/VelvetOpt
Collapse this list.
Dependency lines:
  • velvet>0:biology/velvet
To install the port: cd /usr/ports/biology/velvet/ && make install clean
To add the package: pkg install velvet
PKGNAME: velvet
Flavors: there is no flavor information for this port.
distinfo:

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake : devel/gmake
  2. python2.7 : lang/python27
Runtime dependencies:
  1. python2.7 : lang/python27
  2. perl5>=5.24<5.25 : lang/perl5.24
There are no ports dependent upon this port

Configuration Options

USES:

Master Sites:
  1. http://www.ebi.ac.uk/~zerbino/velvet/

Number of commits found: 17

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
11 Jan 2018 18:09:00
Original commit files touched by this commit  1.2.10_2
Revision:458761
danfe search for other commits by this committer
- Convert to option helper install target (add OPTIONS_DEFINE=DOCS
  when it was missing)
- Invoke INSTALL_DATA where appropriate instead of INSTALL_MAN
- Fix some whitespace and formatting bugs along the way
19 Jan 2015 17:43:58
Original commit files touched by this commit  1.2.10_2
Revision:377443
marino search for other commits by this committer
Designatate 4 ports as unsafe for parallel building

All had similar errors that it couldn't find something during the build,
yet built on a subsequent pass with no adjustments.  Most I've seen before
on previous bulk runs.
26 Nov 2014 13:08:38
Original commit files touched by this commit  1.2.10_2
Revision:373448
mat search for other commits by this committer
Change the way Perl modules are installed, update the default Perl to 5.18.

Before, we had:

  site_perl :           lib/perl5/site_perl/5.18
  site_perl/perl_arch : lib/perl5/site_perl/5.18/mach
  perl_man3 :           lib/perl5/5.18/man/man3

Now we have:

  site_perl : lib/perl5/site_perl
  site_arch : lib/perl5/site_perl/mach/5.18
  perl_man3 : lib/perl5/site_perl/man/man3

Modules without any .so will be installed at the same place regardless of the
(Only the first 15 lines of the commit message are shown above View all of this commit message)
19 Oct 2014 07:38:12
Original commit files touched by this commit  1.2.10_1
Revision:371171
mva search for other commits by this committer
- Convert ports from benchmarks/ and biology/ to new USES=python

Approved by:	portmgr (implicit)
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: 17

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