| Port details |
- velvet Sequence assembler for very short reads
- 1.2.10_2 biology
 =2      1.2.10_2Version of this port present on the latest quarterly branch. - Maintainer: mzaki@m.u-tokyo.ac.jp
- Port Added: 2009-11-07 01:24:24
- Last Update: 2022-09-07 21:58:51
- Commit Hash: fb16dfe
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: not specified in port
- WWW:
- http://www.ebi.ac.uk/~zerbino/velvet/
- Description:
- 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)
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- 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:
- SHA256 (velvet_1.2.10.tgz) = 884dd488c2d12f1f89cdc530a266af5d3106965f21ab9149e8cb5c633c977640
SIZE (velvet_1.2.10.tgz) = 18818559
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- gmake>=4.3 : devel/gmake
- python3.9 : lang/python39
- Runtime dependencies:
-
- python3.9 : lang/python39
- perl5>=5.32.r0<5.33 : lang/perl5.32
- There are no ports dependent upon this port
Configuration Options:- ===> The following configuration options are available for velvet-1.2.10_2:
DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings
- Options name:
- biology_velvet
- USES:
- perl5 gmake shebangfix tar:tgz python
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
07 Sep 2022 21:58:51
 |
Stefan Eßer (se) |
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
|
Stefan Eßer (se) |
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  ) |
1.2.10_2
20 Jul 2022 14:20:57
|
Tobias C. Berner (tcberner) |
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 ) |
1.2.10_2
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
1.2.10_2
11 Jan 2018 18:09:00
 |
danfe |
- 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
|
marino |
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
|
mat |
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 ) |
1.2.10_1
19 Oct 2014 07:38:12
|
mva |
- Convert ports from benchmarks/ and biology/ to new USES=python
Approved by: portmgr (implicit) |
1.2.10_1
29 Jul 2014 19:11:53
|
adamw |
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
|
rakuco |
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
|
rakuco |
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
|
ohauer |
- add stage support |
1.1.04
13 Mar 2014 07:41:34
|
miwi |
- Convert USE_GMAKE to USES |
1.1.04
21 Feb 2014 13:35:26
|
ehaupt |
Remove trailing whitespaces from category biology |
1.1.04
10 Feb 2014 13:54:28
|
ehaupt |
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
|
adamw |
Convert biology to MDOCS and MEXAMPLES |
1.1.04
20 Sep 2013 15:55:44
|
bapt |
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology) |
1.1.04
07 Sep 2013 07:44:27
|
az |
- convert to the new perl5 framework
Approved by: portmgr (bapt@, blanket) |
1.1.04
09 Jun 2011 16:33:21
|
jlaffaye |
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
|
miwi |
- Get Rid MD5 support |
0.7.55
07 Nov 2009 01:23:59
|
amdmi3 |
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> |
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