t_coffee 5.68 biology =1

A multiple DNA or protein sequence alignment package
Maintained by: fernan@iib.unsam.edu.ar
Port Added: 25 Jan 2002 11:58:16
License: not specified in port

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From the website:

  T-Coffee is a multiple sequence alignment package. Given a set of sequences
  (Proteins or DNA), T-Coffee generates a multiple sequence alignment.

  Related publications:
  - 3DCoffee: Combining Protein Sequences and Structures within Multiple
    Sequence Alignments.
    O. O'Sullivan, K Suhre, C. Abergel, D.G. Higgins, C. Notredame.
    Journal of Molecular Biology, Vol 340, pp385-395, 2004
  - T-Coffee: A novel method for multiple sequence alignments.  C.Notredame,
    D. Higgins, J. Heringa, Journal of Molecular Biology,Vol 302,
    pp205-217,2000
  - COFFEE: A New Objective Function For Multiple Sequence Alignmnent.
    C.  Notredame, L. Holme and D.G. Higgins,Bioinformatics,Vol 14 (5)
    407-422,1998

Author: Cedric Notredame <cedric.notredame@europe.com>
WWW: http://www.tcoffee.org/

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

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NOTE: FreshPorts displays only required dependencies information. Optional dependencies are not covered.
Required To Build: biology/clustalw
Required To Run: biology/clustalw
There are no ports dependent upon this port

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

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Configuration Options

     No options to configure

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Master Sites:

http://www.tcoffee.org/Packages/

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

- remove maintainer tags from pkg-descr

Approved by:    portmgr
Approved by:    bapt (mentor)

- Get Rid MD5 support

- Respect PORTDOCS/PORTEXAMPLES

Reported by:    QA Tindie
Approved by:    portmgr

- Update to 5.68
- Remove gcc version restriction

PR:             ports/122435
Submitted by:   Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)

[patch] cleanup non-supported FreeBSD versions

PR:             ports/111728
Submitted by:   Edwin Groothuis <edwin@mavetju.org>
Approved by:    maintainer timeout

- Update to 4.96

PR:             110080
Submitted by:   Fernan Aguero<fernan@iib.unsam.edu.ar> (maintainer)

- Project moves to a new home. Change MASTER_SITES and WWW

PR:             ports/108214
Submitted by:   Thomas Abthorpe <thomas at goodking.ca>
Approved by:    Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)

Update to 3.27.
Use GCC 3.3 on systems with 3.4, due to an internal compiler error.

PR:             ports/93050
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)

Replace ugly "@unexec rmdir %D... 2>/dev/null || true" with @dirrmtry

Approved by:    krion@
PR:             ports/88711 (related)

- Update to 3.18 to make fetchable again
- Mark broken on 6.x upwards

PR:             89977
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
Approved by:    clement (mentor)

BROKEN: Unfetchable

Forced commit to note the port was updated to 3.14 not 3.13

- Update to 3.13. It fixes fetching.

PR:             ports/87264
Submitted by:   maintainer

- Update to 2.03
- Pass maintainership to submitter

PR:             ports/74332
Submitted by:   Fernan Aguero <fernan(at)iib.unsam.edu.ar>

With portmgr hat on, reset inactive maintainer.  These ports are now up
for adoption.

SIZEify (maintainer timeout)

Use the CPIO macro defined in bsd.port.mk.

Use the FIND and XARGS macros introduced in bsd.port.mk 1.391.

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.

Add t_coffee 1.37, a multiple DNA or protein sequence alignment package.    

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