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Port details
t_coffee Multiple DNA or protein sequence alignment package
9.03_3 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

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 25 Jan 2002 11:58:16
License: GPLv2
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

WWW: http://www.tcoffee.org/
SVNWeb : Homepage : PortsMon

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

PKGNAME: t_coffee

distinfo:

SHA256 (T-COFFEE_distribution_Version_9.03.r1318.tar.gz) = 5bb9a531a4036b741a8ff0fe19f3591a3f33bf7ac4f484e5329b1b5dd1fff43c
SIZE (T-COFFEE_distribution_Version_9.03.r1318.tar.gz) = 3455629


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. gfortran48 : lang/gcc
  2. as : devel/binutils
Runtime dependencies:
  1. clustalw : biology/clustalw
  2. gfortran48 : lang/gcc
There are no ports dependent upon this port

Configuration Options
===> The following configuration options are available for t_coffee-9.03_3:
     EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings

USES:
fortran

Master Sites:
  1. http://www.tcoffee.org/Packages/Stable/Version_9.03.r1318/

Number of commits found: 34

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
01 Apr 2016 13:29:17
Original commit files touched by this commit  9.03_3
Revision:412344
mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
14 May 2015 10:15:09
Original commit files touched by this commit  9.03_3
Revision:386312
mat search for other commits by this committer
MASTER_SITES cleanup.

- Replace ${MASTER_SITE_FOO} with FOO.
- Merge MASTER_SITE_SUBDIR into MASTER_SITES when possible. (This means 99.9%
  of the time.)
- Remove occurrences of MASTER_SITE_LOCAL when no subdirectory was present and
  no hint of what it should be was present.
- Fix some logic.
- And generally, make things more simple and easy to understand.

While there, add magic values to the FESTIVAL, GENTOO, GIMP, GNUPG, QT and
SAMBA macros.

Also, replace some EXTRACT_SUFX occurences with USES=tar:*.

Checked by:	make fetch-urlall-list
With hat:	portmgr
Sponsored by:	Absolight
02 Mar 2015 23:09:43
Original commit files touched by this commit  9.03_3
Revision:380301
bapt search for other commits by this committer
Remove Authors from pkg-descr
10 Sep 2014 20:50:37
Original commit files touched by this commit  9.03_3
Revision:367888
gerald search for other commits by this committer
Update the default version of GCC in the Ports Collection from GCC 4.7.4
to GCC 4.8.3.

Part II, Bump PORTREVISIONs.

PR:		192025
Tested by:	antoine (-exp runs)
Approved by:	portmgr (implicit)
09 Jun 2014 11:21:53
Original commit files touched by this commit  9.03_2
Revision:357139
olgeni search for other commits by this committer
Remove indefinite articles and trailing periods from COMMENT, plus
minor COMMENT typos and surrounding whitespace fixes. Categories A-C.

CR:		D196
Approved by:	portmgr (bapt)
10 Mar 2014 20:55:22
Original commit files touched by this commit  9.03_2
Revision:347809
gerald search for other commits by this committer
Update the default version of GCC used in the Ports Collection from
GCC 4.6.4 to GCC 4.7.3.  This entails updating the lang/gcc port as
well as changing the default in Mk/bsd.default-versions.mk.

Part II, Bump PORTREVISIONs.

PR:		182136
Supported by:	Christoph Moench-Tegeder <cmt@burggraben.net> (fixing many ports)
Tested by:	bdrewery (two -exp runs)
18 Dec 2013 17:24:51
Original commit files touched by this commit  9.03_1
Revision:336851
tijl search for other commits by this committer
USES=fortran, staging.
26 Oct 2013 00:52:36
Original commit files touched by this commit  9.03_1
Revision:331644
gerald search for other commits by this committer
Update to libmpc version 1.0.1 which brings the following fixes:

 - Switched to automake 1.11.6, see CVE-2012-3386.
 - #14669: Fixed extraction of CC from gmp.h.
 - Fixed case of intermediate zero real or imaginary part in mpc_fma,
   found by hydra with GMP_CHECK_RANDOMIZE=1346362345.

This is on top of the following changes from version 1.0

 - Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no
   invariant sections) for the documentation.
 - 100% of all lines are covered by tests
 - Renamed functions
   . mpc_mul_2exp to mpc_mul_2ui
   . mpc_div_2exp to mpc_div_2ui
(Only the first 15 lines of the commit message are shown above View all of this commit message)
20 Sep 2013 15:55:44
Original commit files touched by this commit  9.03
Revision:327709
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
14 Aug 2013 22:35:54
Original commit files touched by this commit  9.03
Revision:324744  Sanity Test Failure
ak search for other commits by this committer
- Remove MAKE_JOBS_SAFE variable

Approved by:	portmgr (bdrewery)
14 Jan 2013 08:04:38
Original commit files touched by this commit  9.03
Revision:310361
araujo search for other commits by this committer
- Update to 9.03.

PR:		ports/172499
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
01 Oct 2012 14:45:17
Original commit files touched by this commit  5.68
Revision:305130
tabthorpe search for other commits by this committer
- Reassign to the heap at maintainer's request
10 Jun 2012 18:42:48
Original commit files touched by this commit  5.68
swills search for other commits by this committer
- Convert all remaining instances of BUILD_DEPENDS=${RUN_DEPENDS} or
  RUN_DEPENDS=${BUILD_DEPENDS} to use := which portlint has warned
  about for a while.

PR:             ports/168208
Approved by:    portmgr (miwi)
22 Oct 2011 23:50:23
Original commit files touched by this commit  5.68
eadler search for other commits by this committer
- remove maintainer tags from pkg-descr

Approved by:    portmgr
Approved by:    bapt (mentor)
19 Mar 2011 12:38:54
Original commit files touched by this commit  5.68
miwi search for other commits by this committer
- Get Rid MD5 support
09 Sep 2008 13:43:15
Original commit files touched by this commit  5.68
gahr search for other commits by this committer
- Respect PORTDOCS/PORTEXAMPLES

Reported by:    QA Tindie
Approved by:    portmgr
05 Apr 2008 10:47:12
Original commit files touched by this commit  5.68
rafan search for other commits by this committer
- Update to 5.68
- Remove gcc version restriction

PR:             ports/122435
Submitted by:   Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
02 May 2007 07:15:46
Original commit files touched by this commit  4.96
edwin search for other commits by this committer
[patch] cleanup non-supported FreeBSD versions

PR:             ports/111728
Submitted by:   Edwin Groothuis <edwin@mavetju.org>
Approved by:    maintainer timeout
09 Mar 2007 11:26:16
Original commit files touched by this commit  4.96
miwi search for other commits by this committer
- Update to 4.96

PR:             110080
Submitted by:   Fernan Aguero<fernan@iib.unsam.edu.ar> (maintainer)
22 Jan 2007 23:22:53
Original commit files touched by this commit  3.27
rafan search for other commits by this committer
- 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)
10 Feb 2006 09:45:28
Original commit files touched by this commit  3.27
lawrance search for other commits by this committer
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)
22 Jan 2006 01:25:24
Original commit files touched by this commit  3.18
edwin search for other commits by this committer
Replace ugly "@unexec rmdir %D... 2>/dev/null || true" with @dirrmtry

Approved by:    krion@
PR:             ports/88711 (related)
06 Dec 2005 15:10:08
Original commit files touched by this commit  3.18
tdb search for other commits by this committer
- 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)
28 Oct 2005 06:32:18
Original commit files touched by this commit  3.14
kris search for other commits by this committer
BROKEN: Unfetchable
11 Oct 2005 20:47:02
Original commit files touched by this commit  3.14
sem search for other commits by this committer
Forced commit to note the port was updated to 3.14 not 3.13
11 Oct 2005 20:44:38
Original commit files touched by this commit  3.14
sem search for other commits by this committer
- Update to 3.13. It fixes fetching.

PR:             ports/87264
Submitted by:   maintainer
25 Nov 2004 23:03:54
Original commit files touched by this commit  2.03
sem search for other commits by this committer
- Update to 2.03
- Pass maintainership to submitter

PR:             ports/74332
Submitted by:   Fernan Aguero <fernan(at)iib.unsam.edu.ar>
20 Nov 2004 08:09:49
Original commit files touched by this commit  1.37
linimon search for other commits by this committer
With portmgr hat on, reset inactive maintainer.  These ports are now up
for adoption.
31 Mar 2004 03:12:58
Original commit files touched by this commit  1.37
trevor search for other commits by this committer
SIZEify (maintainer timeout)
22 Jan 2004 12:18:43
Original commit files touched by this commit  1.37
trevor search for other commits by this committer
Use the CPIO macro defined in bsd.port.mk.
13 Nov 2003 14:45:08
Original commit files touched by this commit  1.37
trevor search for other commits by this committer
Use the FIND and XARGS macros introduced in bsd.port.mk 1.391.
22 Oct 2003 09:29:55
Original commit files touched by this commit  1.37
osa search for other commits by this committer
Cosmetic fix: use %%DOCSDIR%% macro.
No functionally changes.

Submitted by:   Oleg Karachevtsev <ok@etrust.ru>
A part of PR:   57992
07 Mar 2003 05:56:43
Original commit files touched by this commit  1.37
ade search for other commits by this committer
Clear moonlight beckons.
Requiem mors pacem pkg-comment,
And be calm ports tree.

E Nomini Patri, E Fili, E Spiritu Sancti.
25 Jan 2002 14:58:16
files touched by this commit
wjv search for other commits by this committer
Add t_coffee 1.37, a multiple DNA or protein sequence alignment package.    

Number of commits found: 34

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