fasta3 35.3.6 biology =1

NO CDROM: May not be sold or incorporated into a commercial product
A collection of programs for searching DNA and protein databases
Maintained by: fernan@iib.unsam.edu.ar
Port Added: 11 Feb 2001 13:29:00

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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.

Author: William R Pearson <wrp@virginia.edu>
WWW:    http://fasta.bioch.virginia.edu/

-- Johann Visagie <johann@egenetics.com>

CVSWeb : Sources : Main Web Site : Distfiles Availability : PortsMon

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To install the port: cd /usr/ports/biology/fasta3/ && make install clean
To add the package: pkg_add -r fasta3

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Configuration Options

     No options to configure

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Master Sites:

http://faculty.virginia.edu/wrpearson/fasta/fasta3/

ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/

- Update to 35.3.6

PR:             ports/122607
Submitted by:   maintainer (Fernan Aguero)

- 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)

- Update to 34.26.2

PR:             110079
Submitted by:   Fernan Aguero<fernan@iib.unsam.edu.ar> (maintainer)

- Update to 34.t26.b3

PR:             ports/104508
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)

- Update to 34.t25.d9

PR:             ports/98761
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)

- 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]

- update to 34.t25.d7
- add MASTER_SITE_LOCAL as a second master site

PR:             ports/97310
Submitted by:   maintainer

BROKEN: Unfetchable

- Update to 34.t25.d6

PR:             ports/96063
Submitted by:   maintainer

- Update to 34.t25.d5

PR:             ports/94741
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)

Update to 34.t25.d4.

PR:             ports/93052
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)

SHA256ify

Approved by:    krion@

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>

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.

SIZEify (maintainer timeout)

BROKEN: Checksum mismatch

unPERLify by using REINPLACE_CMD and SED where appropriate.

PR:             47654
Submitted by:   Simon 'portlint' Schubert <corecode@corecode.ath.cx>

Cosmetic fix: use %%DOCSDIR%% macro.
No functionally changes.

Submitted by:   Oleg Karachevtsev <ok@etrust.ru>
A part of PR:   57992

Clear moonlight beckons.
Requiem mors pacem pkg-comment,
And be calm ports tree.

E Nomini Patri, E Fili, E Spiritu Sancti.

Prefer <limits.h> over <values.h> as the latter has been removed from
-current.

Noticed by:     bento

Replace erroneous usage of INSTALL_MAN with INSTALL_DATA.    

Updating my email address in my remaining ports.    

Updata biology/fasta3 to version 33.t08.d4    

Update to 33.t08.d3.    

- A small bugfix lead to a rerelease without a version number change.   - Bumped
PORTREVISION.    

update to 33.t08.d2.    

- 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)    

8 vulnerabilities affecting 22 ports have been reported in the past 14 days

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