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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 View this port on Repology. pkg-fallout Version 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: 2022-09-07 21:58:51
Commit Hash: fb16dfe
License: not specified in port
Description:
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb
pkg-plist: as obtained via: make generate-plist
Expand this list (23 items)
Collapse this list.
  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, run one of these commands:
  • pkg install biology/velvet
  • pkg install velvet
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: velvet
Flavors: there is no flavor information for this port.
distinfo:

Packages (timestamps in pop-ups are UTC):
velvet
ABIlatestquarterly
FreeBSD:11:aarch641.2.10_21.2.10_2
FreeBSD:11:amd641.2.10_21.2.10_2
FreeBSD:11:armv61.2.10_21.2.10_2
FreeBSD:11:i3861.2.10_21.2.10_2
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips641.2.10_21.2.10_2
FreeBSD:12:aarch641.2.10_21.2.10_2
FreeBSD:12:amd641.2.10_21.2.10_2
FreeBSD:12:armv61.2.10_21.2.10_2
FreeBSD:12:armv71.2.10_21.2.10_2
FreeBSD:12:i3861.2.10_21.2.10_2
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips641.2.10_21.2.10_2
FreeBSD:12:powerpc64pkg-fallout1.2.10_2
FreeBSD:13:aarch641.2.10_21.2.10_2
FreeBSD:13:amd641.2.10_21.2.10_2
FreeBSD:13:armv61.2.10_21.2.10_2
FreeBSD:13:armv71.2.10_21.2.10_2
FreeBSD:13:i3861.2.10_21.2.10_2
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc641.2.10_21.2.10_2
FreeBSD:13:riscv64pkg-fallout1.2.10_2
FreeBSD:14:aarch641.2.10_2pkg-fallout
FreeBSD:14:amd641.2.10_2pkg-fallout
FreeBSD:14:armv61.2.10_2pkg-fallout
FreeBSD:14:armv71.2.10_2pkg-fallout
FreeBSD:14:i3861.2.10_2pkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc641.2.10_2pkg-fallout
FreeBSD:14:riscv641.2.10_2pkg-fallout
 
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake>=4.3 : devel/gmake
  2. python3.9 : lang/python39
Runtime dependencies:
  1. python3.9 : lang/python39
  2. perl5>=5.32.r0<5.33 : lang/perl5.32
There are no ports dependent upon this port

Configuration Options:
Options name:
USES:
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. http://www.ebi.ac.uk/~zerbino/velvet/
Collapse this list.

Number of commits found: 21

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
07 Sep 2022 21:58:51
commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
1.2.10_2
07 Sep 2022 21:10:59
commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
1.2.10_2
20 Jul 2022 14:20:57
commit hash:37526bbd4e50616d87f70e1c788ae4895d88d671commit hash:37526bbd4e50616d87f70e1c788ae4895d88d671commit hash:37526bbd4e50616d87f70e1c788ae4895d88d671commit hash:37526bbd4e50616d87f70e1c788ae4895d88d671 files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
biology: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>
(Only the first 15 lines of the commit message are shown above View all of this commit message)
1.2.10_2
06 Apr 2021 14:31:07
commit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
1.2.10_2
11 Jan 2018 18:09:00
Revision:458761Original commit files touched by this commit
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
1.2.10_2
19 Jan 2015 17:43:58
Revision:377443Original commit files touched by this commit
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.
1.2.10_2
26 Nov 2014 13:08:38
Revision:373448Original commit files touched by this commit
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)
1.2.10_1
19 Oct 2014 07:38:12
Revision:371171Original commit files touched by this commit
mva search for other commits by this committer
- Convert ports from benchmarks/ and biology/ to new USES=python

Approved by:	portmgr (implicit)
1.2.10_1
29 Jul 2014 19:11:53
Revision:363374Original commit files touched by this commit
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)
1.2.10_1
20 Jun 2014 12:54:29
Revision:358567Original commit files touched by this commit
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)
1.2.10
17 Jun 2014 21:39:44
Revision:358183Original commit files touched by this commit
rakuco search for other commits by this committer
Update to 1.2.10.

PR:		191129
Submitted by:	mzaki@m.u-tokyo.ac.jp (maintainer)
1.1.04
01 Jun 2014 11:33:57
Revision:356099Original commit files touched by this commit
ohauer search for other commits by this committer
- add stage support
1.1.04
13 Mar 2014 07:41:34
Revision:348042Original commit files touched by this commit
miwi search for other commits by this committer
- Convert USE_GMAKE to USES
1.1.04
21 Feb 2014 13:35:26
Revision:345397Original commit files touched by this commit
ehaupt search for other commits by this committer
Remove trailing whitespaces from category biology
1.1.04
10 Feb 2014 13:54:28
Revision:343634Original commit files touched by this commit
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)
1.1.04
03 Jan 2014 15:46:52
Revision:338550Original commit files touched by this commit
adamw search for other commits by this committer
Convert biology to MDOCS and MEXAMPLES
1.1.04
20 Sep 2013 15:55:44
Revision:327709Original commit files touched by this commit
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
1.1.04
07 Sep 2013 07:44:27
Revision:326575Original commit files touched by this commit
az search for other commits by this committer
- convert to the new perl5 framework

Approved by:	portmgr (bapt@, blanket)
1.1.04
09 Jun 2011 16:33:21
Original commit files touched by this commit
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)
0.7.55
19 Mar 2011 12:38:54
Original commit files touched by this commit
miwi search for other commits by this committer
- Get Rid MD5 support
0.7.55
07 Nov 2009 01:23:59
Original commit files touched by this commit
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: 21