Port details |
- fasta3 Collection of programs for searching DNA and protein databases
- 36.3.8_1 biology =2 36.3.8_1Version of this port present on the latest quarterly branch.
- Maintainer: wendell@bsd.com.br
- Port Added: 2001-02-11 13:29:00
- Last Update: 2024-01-10 08:16:01
- Commit Hash: 1b819e4
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: Fasta
- WWW:
- http://fasta.bioch.virginia.edu/
- Description:
- Version 3 of the FASTA packages contains many programs for searching DNA and
protein databases and one program (prss3) for evaluating statistical
significance from randomly shuffled sequences. Several additional analysis
programs, including programs that produce local alignments, are available as
part of version 2 of the FASTA package, which is available as the port
biology/fasta.
FASTA is described in: W. R. Pearson and D. J. Lipman (1988), "Improved
Tools for Biological Sequence Analysis", PNAS 85:2444-2448; W. R. Pearson
(1996) "Effective protein sequence comparison" Meth. Enzymol. 266:227-258;
Pearson et. al. (1997) Genomics 46:24-36; Pearson, (1999) Meth. in
Molecular Biology 132:185-219.
The FASTA3 suite is distributed freely subject to the condition that it may
not be sold or incorporated into a commercial product.
- ¦ ¦ ¦ ¦
- 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/fasta3/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/fasta3
- pkg install fasta3
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: fasta3
- Flavors: there is no flavor information for this port.
- distinfo:
- SHA256 (fasta3/2014-01-29/fasta-36.3.8.tar.gz) = e235458afd16591bbcd5b89b639497e20346841091440a2445593318510a2262
SIZE (fasta3/2014-01-29/fasta-36.3.8.tar.gz) = 1211304
Packages (timestamps in pop-ups are UTC):
- This port has no dependencies.
- There are no ports dependent upon this port
Configuration Options:
- ===> The following configuration options are available for fasta3-36.3.8_1:
DOCS=on: Build and/or install documentation
EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings
- Options name:
- biology_fasta3
- 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 |
36.3.8_1 10 Jan 2024 08:16:01 |
Baptiste Daroussin (bapt) |
MAN?PREFIX: eleminate its usage and move man to share/man |
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) |
36.3.8 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 ) |
36.3.8 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 ) |
36.3.8 06 May 2021 11:47:41 |
Mathieu Arnold (mat) |
Deorbit RESTRICTED && NO_CDROM, part one.
For ports that already use the licenses framwork, merge the content of
RESTRICTED/NO_CDROM/LEGAL* entries into LICENSEs.
Approved by: rene
Differential Revision: https://reviews.freebsd.org/D30010 |
36.3.8 06 Apr 2021 14:31:07 |
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
36.3.8 13 Aug 2019 16:00:39 |
mat |
Convert to UCL & cleanup pkg-message (categories a-c) |
36.3.8 19 May 2016 11:09:14 |
amdmi3 |
- Fix trailing whitespace in pkg-messages
Approved by: portmgr blanket |
36.3.8 16 Oct 2015 13:31:10 |
danilo |
- Update to 36.3.8
- Pass maintainership to submitter
PR: 203817
Submitted by: Wendell Borges <wendell@bsd.com.br> |
36.3.7a 07 May 2015 02:33:58 |
wen |
- Update to 36.3.7a |
36.3.6d_1 20 Oct 2014 07:10:48 |
bapt |
Cleanup plist |
36.3.6d_1 02 Mar 2014 10:58:50 |
marino |
biology/fasta3: Checked new distfile and regenerated distinfo to unbreak
Fasta3 distfile was significantly changed. This should have been released
as a new version (e.g. 36.3.6e), so it's not clear why the distfile was
rerolled. There are significant changes to makefiles, conf files and even
a few .c and .h files. They all look like legitimate updates to me
though.
Set DIST_SUBDIR since this port is now known for rerolling, then
regenerate distinfo. Also add Fasta license and bump revision. |
36.3.6d 03 Jan 2014 19:46:05 |
bapt |
Mark as broken: Invalid checksum, seems like the software was rerolled |
36.3.6d 29 Oct 2013 19:32:16 |
pawel |
Update to version 36.3.6d
PR: ports/181883
Submitted by: KATO Tsuguru <tkato432@yahoo.com> |
36.3.6 20 Sep 2013 15:55:44 |
bapt |
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology) |
36.3.6 07 Sep 2013 17:20:21 |
sunpoet |
- Use single space after WWW: |
36.3.6 19 Jul 2013 14:08:02 |
wen |
- Update to 36.3.6
- Drop maintainership |
36.3.2 01 Oct 2012 14:55:55 |
wen |
- Take maintainership |
36.3.2 01 Oct 2012 14:45:17 |
tabthorpe |
- Reassign to the heap at maintainer's request |
36.3.2 22 Oct 2011 23:50:23 |
eadler |
- remove maintainer tags from pkg-descr
Approved by: portmgr
Approved by: bapt (mentor) |
36.3.2 26 Jan 2011 20:26:36 |
beat |
- Update to 36.3.2 to fix distfile fetching on pointyhat
PR: ports/154267
Submitted by: Fernan Aguero <fernan AT iib.unsam.edu.ar> (maintainer)
Feature safe: yes |
35.4.9 23 Aug 2009 15:47:37 |
makc |
Update to 35.4.9
PR: ports/137991
Submitted by: Fernan Aguero (maintainer) |
35.4.7 09 Jun 2009 07:53:37 |
itetcu |
- Update to 35.4.7 [1]
- Obey PREFIX [2]
Submitted by: maintainer [1] [2]
Reported by: QATty [2] |
35.4.4 23 Feb 2009 16:13:19 |
amdmi3 |
- Add forgotten patch |
35.4.4 23 Feb 2009 16:12:23 |
amdmi3 |
- Update to 35.4.4
PR: 132007
Submitted by: Fernan Aguero <fernan at iib dot unsam dot edu dot ar>
(maintainer) |
35.3.6 10 Apr 2008 08:09:10 |
clsung |
- Update to 35.3.6
PR: ports/122607
Submitted by: maintainer (Fernan Aguero) |
35.3.5 30 Mar 2008 05:07:37 |
rafan |
- Update to 35.3.5
- Switch to .tar.gz distfile so that we don't define our do-extract
- While I'm here, using substitution for version numbers in pkg-plist
for easier upgrade
PR: ports/121690
Submitted by: Wen heping <wenheping at gmail.com>
Approved by: maintainer timeout (2 weeks) |
34.26.2 09 Mar 2007 11:26:13 |
miwi |
- Update to 34.26.2
PR: 110079
Submitted by: Fernan Aguero<fernan@iib.unsam.edu.ar> (maintainer) |
34.t26.b3 31 Oct 2006 09:02:04 |
miwi |
- Update to 34.t26.b3
PR: ports/104508
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) |
34.t25.d9 09 Jun 2006 19:18:08 |
pav |
- Update to 34.t25.d9
PR: ports/98761
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) |
34.t25.d8 05 Jun 2006 21:18:24 |
erwin |
- Update to 34.t25.d8 [1]
- While I'm here, pet portlint [2]
PR: 98398 [1]
Submitted by: miwi [1], self [2]
Approved by: maintainer [1] |
34.t25.d7 24 May 2006 16:55:46 |
sem |
- update to 34.t25.d7
- add MASTER_SITE_LOCAL as a second master site
PR: ports/97310
Submitted by: maintainer |
34.t25.d6 21 May 2006 21:32:08 |
kris |
BROKEN: Unfetchable |
34.t25.d6 07 May 2006 16:52:33 |
sem |
- Update to 34.t25.d6
PR: ports/96063
Submitted by: maintainer |
34.t25.d5 20 Mar 2006 22:23:24 |
pav |
- Update to 34.t25.d5
PR: ports/94741
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) |
34.t25.d4 10 Feb 2006 09:37:02 |
lawrance |
Update to 34.t25.d4.
PR: ports/93052
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) |
33.t08.d4 22 Jan 2006 08:20:34 |
edwin |
SHA256ify
Approved by: krion@ |
33.t08.d4 01 Jul 2004 03:02:23 |
linimon |
Chase mastersite and fix checksum to unbreak. (Changes are inclusion of a
logfile, one Linux-only change, and one change in a test script). Assign
submitter as new maintainer as current one has not responded to PRs for
some time.
PR: ports/68199
Submitted by: Fernan Aguero <fernan at iib dot unsam dot edu dot ar> |
33.t08.d4 21 Jun 2004 21:27:46 |
kris |
Set an expiry date of 2004-08-20 for these BROKEN/IGNORE/FORBIDDEN
ports. They will be removed on or after that date if they are still
broken and no fix has been submitted to GNATS. |
33.t08.d4 31 Mar 2004 03:12:58 |
trevor |
SIZEify (maintainer timeout) |
33.t08.d4 21 Feb 2004 19:31:10 |
kris |
BROKEN: Checksum mismatch |
33.t08.d4 15 Nov 2003 20:13:21 |
marcus |
unPERLify by using REINPLACE_CMD and SED where appropriate.
PR: 47654
Submitted by: Simon 'portlint' Schubert <corecode@corecode.ath.cx> |
33.t08.d4 22 Oct 2003 09:29:55 |
osa |
Cosmetic fix: use %%DOCSDIR%% macro.
No functionally changes.
Submitted by: Oleg Karachevtsev <ok@etrust.ru>
A part of PR: 57992 |
33.t08.d4 07 Mar 2003 05:56:43 |
ade |
Clear moonlight beckons.
Requiem mors pacem pkg-comment,
And be calm ports tree.
E Nomini Patri, E Fili, E Spiritu Sancti. |
33.t08.d4 23 Aug 2002 03:36:33 |
kris |
Prefer <limits.h> over <values.h> as the latter has been removed from
-current.
Noticed by: bento |
03 Jul 2001 10:08:26 |
wjv |
Replace erroneous usage of INSTALL_MAN with INSTALL_DATA. |
27 Jun 2001 11:15:02 |
wjv |
Updating my email address in my remaining ports. |
07 May 2001 13:16:33 |
jeh |
Updata biology/fasta3 to version 33.t08.d4 |
22 Mar 2001 09:04:47 |
sobomax |
Update to 33.t08.d3. |
12 Mar 2001 10:24:38 |
nbm |
- A small bugfix lead to a rerelease without a version number change. - Bumped
PORTREVISION. |
08 Mar 2001 14:39:17 |
sf |
update to 33.t08.d2. |
11 Feb 2001 16:29:00 |
jeh |
- New port: biology/fasta3, which comprises the FASTA3 suite of DNA and
protein sequence search programs - FASTA3 updates only some of the elements of
FASTA2, which is why I have submitted ports of both versions (as
biology/fasta and biology/fasta3) |