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Commit Graph

783 Commits

Author SHA1 Message Date
Pav Lucistnik
eb9164cdb6 - Provide SSE optimized application as an option 2006-06-24 21:04:45 +00:00
Pav Lucistnik
ac3d6b8aa7 - Instruct amd64 users to libmap libpthread.so.2 to libc_r.so.6 2006-06-22 18:53:30 +00:00
Pav Lucistnik
15299a017f SIMAP (Similarity Matrix of Proteins) is a public database of pre-calculated
protein similarities that plays a key role in many bioinformatics methods. It
contains about all currently published protein sequences and is continuously
updated.

The computational effort for keeping SIMAP up-to-date is constantly increasing.
Please help to update SIMAP by calculating protein similarities on your
computer.

WWW: http://boinc.bio.wzw.tum.de/boincsimap/
2006-06-19 20:32:08 +00:00
Thierry Thomas
57359d2a70 Re-add CONFIGURE_TARGET and fix libm detection.
PR:		ports/99072 (fu2)
Submitted by:	Josh Tolbert <hemi (at) puresimplicity.net> (maintainer)
2006-06-18 20:35:18 +00:00
Thierry Thomas
78ba726349 - Upgrade to to 1.9.9 and unbreak;
- Take maintainership.

PR:		ports/99072
Submitted by:	Josh Tolbert <hemi (at) puresimplicity.net>
2006-06-17 22:07:36 +00:00
Erwin Lansing
0ca34eb9ed USE_SIZE was obsoleted in rev. 1.484 of bsd.port.mk more than
2 years ago. Clean out the last traces of it.

With hat:	portmgr
2006-06-11 15:29:01 +00:00
Pav Lucistnik
e6e4d55131 - Update PORTREVISION to match latest release (see main web site)
- Update the port to add other architectures (amd64)

PR:		ports/98764
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
2006-06-11 09:13:43 +00:00
Pav Lucistnik
3181cf2cce - Update to 34.t25.d9
PR:		ports/98761
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
2006-06-09 19:18:08 +00:00
Ion-Mihai Tetcu
9da018b5cc Update biology/ncbi-toolkit to the latest release.
Quoting from www.ncbi.nlm.nih.gov/blast/blast_whatsnew.shtml
Major changes include:
 blastall now uses the new engine by default, resulting
 in significant performance improvements and enabling
 query concatenation for all program types.

PR:		ports/98570
Submitted by:	maintainer
Approved by:	lawrance (mentor, implict)
2006-06-06 12:05:19 +00:00
Erwin Lansing
f85047fc66 - Add MASTER_SITE
- Use DATADIR

PR:		97603
Submitted by:	miwi
Approved by:	maintainer timeout
2006-06-06 10:07:55 +00:00
Erwin Lansing
f0dcdd522f - 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]
2006-06-05 21:18:23 +00:00
Sergey Matveychuk
45d46bd0a5 - update to 34.t25.d7
- add MASTER_SITE_LOCAL as a second master site

PR:		ports/97310
Submitted by:	maintainer
2006-05-24 16:55:46 +00:00
Kris Kennaway
b8bfb594a1 BROKEN: Unfetchable 2006-05-21 21:40:02 +00:00
Sergey Matveychuk
2e790c2143 - Update to 3.15
PR:		ports/96941
Submitted by:	Paul Schmehl <pauls@utdallas.edu>
Approved by:	maintainer timeout
2006-05-20 18:52:19 +00:00
Aaron Dalton
e25d96e450 - Updated from 0.07 to 0.12
Approved by:	tobez (implicit)

0.08 20/Feb/2006 15:14
                       Improved referential integrity between nodes,
                                taxa, and data.
                       Implemented Fastnexus parser
                       Node object silently implements Bio::Tree::NodeI
                       		interface if BioPerl is installed
                       Tree object silently implements Bio::Tree::TreeI
                       		interface if BioPerl is installed
                       Added convertor methods for XML and CIPRES
                       Implemented more Matrix methods
                       Implemented symbol tables in Bio::Phylo::Util::CONSTANT
                       Implemented visit method for listable objects
                       Implemented caching infrastructure for calculations
                       Changed object-model to inside-out arrays
                       Added Biodiversity measures code by Aki Mimoto
                       Moved constants and exceptions to Bio::Phylo::Util::*
                       Fixed memory leak due to circular references
2006-05-19 23:18:32 +00:00
Aaron Dalton
29ad3c789c Adding port biology/p5-Bio-Phylo, Phylogenetic analysis using perl.
Approved by:	tobez (implicit)
2006-05-13 16:48:15 +00:00
Sergey Matveychuk
edab74313c - Update to 34.t25.d6
PR:		ports/96063
Submitted by:	maintainer
2006-05-07 16:52:33 +00:00
Sam Lawrance
649566ad8c Update to 21.u1.d1 (fixes fetch).
Reported by:	fenner's distfile survey
2006-05-07 13:04:20 +00:00
Sergey Matveychuk
36778a1acd - Satisfy portlint 2006-05-06 21:20:59 +00:00
Emanuel Haupt
dfc2535ebe Add protomol 2.0.3, OO, component based, framework for molecular
dynamics (MD) simulations.

PR:		95123
Submitted by:	Sangwoo Shim <sangwoos@gmail.com>
2006-05-05 20:09:54 +00:00
Edwin Groothuis
72ad491a93 Remove USE_REINPLACE from all categories starting with B 2006-05-03 23:26:35 +00:00
Yen-Ming Lee
fb9e59f589 - Update to 1.89
- refine BROKEN to make portlint happier
- patch to use on Scalar::Util instead of WeakRef
- mark IGNORE under old perl which don't support weak reference

PR:		96656
Submitted by:	leeym
Approved by:	maintainer
2006-05-02 23:16:02 +00:00
Renato Botelho
8aaa665368 Bioperl-run contain modules that provides a PERL interface to various
bioinformatics applications. This allows various applications to be used
with common Bioperl objects.

WWW: http://bioperl.org/

PR:		ports/93675
Submitted by:	Mauricio Herrera Cuadra <mauricio@arareko.net>
2006-05-02 21:31:43 +00:00
Renato Botelho
5d19d83aa6 Bioperl-run contain modules that provides a PERL interface to various
bioinformatics applications. This allows various applications to be used
with common Bioperl objects.

WWW: http://bioperl.org/

PR:		ports/93674
Submitted by:	Mauricio Herrera Cuadra <mauricio@arareko.net>
2006-05-02 21:30:08 +00:00
Pav Lucistnik
dc8e5f28fa - Update to 1.0.0
- Provide OPTIONS
- Take maintainership

PR:		ports/94123
Submitted by:	Mauricio Herrera Cuadra <mauricio@arareko.net>
2006-04-25 22:09:29 +00:00
Kris Kennaway
87b2bd6cb6 BROKEN: Does not compile 2006-04-22 22:10:17 +00:00
Mark Linimon
54a45e213c Reset rmiya@cc.hirosaki-u.ac.jp who has not responded to email asking about
maintainer timeouts.

Hat:	portmgr
2006-04-05 06:13:46 +00:00
Mark Linimon
756130dd96 Reset jeremy@external.org who has not responded to email asking about
maintainer timeouts.

Hat:	portmgr
2006-04-05 05:46:33 +00:00
Marcus Alves Grando
843d1a4279 - Update to 2006.02.13
PR:		95281
Submitted by:	maintainer
2006-04-05 01:58:03 +00:00
Edwin Groothuis
c88ecfb4d6 Use SUB_FILES for pkg-message 2006-04-01 12:34:24 +00:00
Thierry Thomas
10570c91c8 For EMBOSS:
This patch brings EMBOSS up to date with the current version.

	i.   The patches included in files/ are bugfixes for files in
	     EMBOSS-3.0.0 that appeared after the release. They are
   	     documented in ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README

	     This is just 'for the record' so that we remember to remove these
	     patches in the next update.

	ii.  EMBOSS is now installed by default in LOCALBASE/emboss
	     This is to avoid CONFLICTS with other ports that install files
	     with the same names. Installing EMBOSS to another PREFIX is also
	     possible.

	iii. now EMBASSY and EMBOSS both store their distfiles in the same
	     DIST_SUBDIR

	iv.  use built-in PKGMESSAGE and SUB_FILES instead of doing it the old
	     (manual) way

	For EMBASSY:

	This update brings embassy in sync with the update of EMBOSS to 3.0.0.

	Things that changed from previous version of the port:

	i.  embassy now installs by default in $LOCALBASE/emboss (the
	    new default PREFIX for emboss as well).

	ii. changed DIST_SUBDIR so that all the distfiles are put together with
	    emboss. This makes sense(TM)

	iii. incorporated new EMBASSY apps (this accounts for the changes in
	     OPTIONS and pkg-plist)

	iv.  removed obsoleted patches

	Finally, I included a sample text that could go in UPDATING.

PR:		93053
Submitted by:	Fernan Aguero <fernan (at) iib.unsam.edu.ar> (maintainer)
2006-03-31 09:43:21 +00:00
Pav Lucistnik
763955a476 - Update to 34.t25.d5
PR:		ports/94741
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
2006-03-20 22:23:24 +00:00
Renato Botelho
c1c9dc017a - Update to 5.743
- Add a MASTER_SITE backup since oficial one just have last version and make
  it fetchable again

Submitted by:	maintainer by email
Reported by:	krismail
2006-03-19 12:59:16 +00:00
Renato Botelho
35642ebc86 Add lagan 1.2, efficient tools for large-scale multiple alignments of
genomic DNA.

PR:		ports/93058
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
2006-03-16 22:31:26 +00:00
Renato Botelho
81ba48cd37 Add mafft 5.734, multiple sequence alignments based on fast Fourier
transform.

PR:		ports/93059
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
2006-03-15 10:41:16 +00:00
Renato Botelho
1b3445b684 Add dotter 20021204 # last modified date in FTP server, a viewer for
multiple sequence alignments.

PR:		ports/93055
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
2006-03-15 10:35:24 +00:00
Renato Botelho
0694735737 Add blat 33, a fast tool for local sequence similarity searches.
PR:		ports/93060
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
2006-03-15 10:26:12 +00:00
Renato Botelho
bfe1c1f260 Add belvu 2.29, a viewer for multiple sequence alignments.
PR:		ports/93056
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
2006-03-15 10:24:57 +00:00
Maho Nakata
a8bac6a90f Update to 1.5
Submitted by:	distfile survey by kris, fenner
2006-03-15 08:10:49 +00:00
Ade Lovett
fe279f0df8 Bump PORTREVISION on glib12/gtk12 consumer ports to ease the upgrade path.
Discussed with:	kris
Approved by:	portmgr (implicit)
2006-03-07 08:28:06 +00:00
Ade Lovett
8503536d38 Conversion to a single libtool environment.
Approved by:	portmgr (kris)
2006-02-23 10:40:44 +00:00
Kris Kennaway
65fe00966b BROKEN: Configure fails 2006-02-20 01:46:03 +00:00
Herve Quiroz
cf01181180 Jalview is a multiple alignment editor written in Java. It is used widely in a
variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain
database) and is also available as a general purpose alignment editor.

WWW: http://www.jalview.org

PR:		93054
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
2006-02-13 09:42:13 +00:00
Alexander Leidinger
d16f7bfb92 Reset maintainership to ports@ after ~4 months without any response to any
PR.

Thanks for contributing.

Since the acroread7 port is a somewhat important port for our users, I
will hand it over to emulation@ if no _active_ *committer* takes it
before the ports freeze.

While I'm here:
 - fix a little nit in the csound port (I think the intention was to
   create no backup file instead of creating one with a "-e" extension)
 - set ARCH to i386 in the amd64 case for the acroread7 port. This
   is a work-around to be able to install everything when a dependency
   is not already installed (ARCH is read-only in sub-makes, so the
   dependencies can't change it). This should be removed when the
   dependencies are fixed or converted to use bsd.linux-rpm.mk. [1]

Not objected to by:	portmgr (explicit: krion; silence: rest)
Maintainer timeout:	~4 months
Submitted by:		Sangwoo Shim <sangwoos@gmail.com> [1]
PR:			87985 [1]
2006-02-11 21:03:14 +00:00
Sam Lawrance
0e94382809 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)
2006-02-10 09:45:28 +00:00
Sam Lawrance
f4cdc25a87 Update to 34.t25.d4.
PR:		ports/93052
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
2006-02-10 09:37:02 +00:00
Sam Lawrance
fed5ed01f9 Update to 2006.01.25.
PR:		ports/93051
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
2006-02-09 10:33:47 +00:00
Sam Lawrance
c70bfb8977 Put PORTEPOCH back.
Reported by:	chkversion
2006-02-09 01:17:59 +00:00
Sam Lawrance
c6f127a070 Update to 3.65.
PR:		ports/92182
Submitted by:	"Choe, Cheng-Dae" <whitekid@gmail.com>
Approved by:	dbader@ece.unm.edu (maintainer, timeout 14 days)
2006-02-08 14:45:45 +00:00
Joe Marcus Clarke
92cc33210c Remove CONFLICTS with nss. 2006-02-02 23:12:05 +00:00