- 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)
- Add RESTRICTED due to a non-commercial use licence.
PR: ports/121794
Submitted by: KATO Tsuguru <tkato432@yahoo.com>
Approved by: thierry and tabthorpe (mentors)
Bayesian inference of phylogeny is based upon a quantity called the
posterior probability distribution of trees, which is the probability of a
tree conditioned on the observations. The conditioning is accomplished
using Bayes's theorem. The posterior probability distribution of trees is
impossible to calculate analytically; instead, MrBayes uses a simulation
technique called Markov chain Monte Carlo (or MCMC) to approximate the
posterior probabilities of trees.
WWW: http://mrbayes.csit.fsu.edu/
PR: ports/118542
Submitted by: mzaki at biol.s.u-tokyo.ac.jp
or draft sequence. This package provides an efficient suffix tree library,
seed-and-extend alignment, SNP detection, repeat detection, and
visualization tools.
WWW: http://mummer.sourceforge.net/
PR: ports/118142
Submitted by: Tony Maher
(also: update to 5.0.4)
Upon installing FoldingAtHome I ran the software from a
user account only to find that I was stuck in a loop of
trying to enter configuration options. Shortly thereafter
I realized that it was trying to write to
/usr/local/share/foldingathome, and therefore requires being
run as root to write there unless one changes permissions
there. Seing as this isn't installed with a startup script
for daemonization, and running as root seems a little
excessive for this application, should this be adapted to
run from a user account or set up to be able to start at
boot?
And from maintainer:
This diff updates the port to version 5.04, and adds
support to running as normal user using ~/.fah
directory.
PR: ports/113335
Submitted by: James Snyder <jbsnyder@fanplastic.org>
Approved by: maintainer
- Don't install CVS directories which are going to be removed
in next release
PR: ports/113831
Submitted by: Thomas Abthorpe <thomas at goodking.ca>
Approved by: maintainer timeout (20 days)
2007-01-07 biology/coalesce: distfile disappeared from homepage
Actually the software is still available at:
http://evolution.gs.washington.edu/lamarc/coalesce.html, but it is
not supported by the authors. Last version is from 1995 and
biology/fluctuate can be used instead.
. bump PORTREVISION (RUN_DEPENDS changes);
. for converters/konwert:
- introduce PATCHLEVEL to be used instead of PORTREVISION at filenames;
- update to new PATCHLEVEL=11.
PR: 107000 [1], 107046 [2], 107106 [3], 107114 [4]
Submitted by: bsam (me)
Approved by: all maintainers timeout three and a half week:
mij at bitchx.it [1]
j.koopmann at seceidos.de [2]
chuynh at biolateral.com.au [3]
alexs at snark.rinet.ru [4]
support for reading and writing BEAST, Clustal, EMBL, Fasta, GCG-MSF, GDE,
Hennig86, NCBI, NEXUS, NONA, PDB, Phylip, PIR, Plain/Raw, Swiss-Prot and
TNT files by writing only three lines of code.
The framework is written in Cocoa (Objective-C).
WWW: http://bioinformatics.org/biococoa/
world download and run software to band together to make one of the largest
supercomputers in the world. Every computer makes the project closer to our
goals.
Folding@Home uses novel computational methods coupled to distributed computing,
to simulate problems thousands to millions of times more challenging than
previously achieved.
WWW: http://folding.standford.edu
PR: ports/101235
Submitted by: Yonatan <onatan@gmail.com>
o add data dir to have working port[1]
PR: 95121[1]
Submitted by: Sangwoo Shim <sangwoos at gmail.com>[1]
This commit is a result of hacks at the CodeFest Akihabara 2006 hosted by FSIJ.
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/
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)
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
- 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
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>
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>
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)
- 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
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>
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]
unnecessary PORTEPOCH bump)
- Update MASTER_SITES and WWW line, provide backup download site
- Come up with better port description
- Reset maintainer to ports@
- Uphold CXX and CXXFLAGS
- Clean up Makefile slightly
- Don't install yet another copy of GPL and texts in French
- Add SHA256 hash to distinfo
- Shared lib version and PORTREVISION bumb for all affected ports.
While I'm here:
- Remove USE_MESA knob where it was (35 ports).
It marked as depricated for 2 years.
PR: ports/90247
Submitted by: Ermal Lu?i <eri--@albabsd.org>
From: Tony Maher <anthony.maher@uts.edu.au>
To: Edwin Groothuis <edwin@FreeBSD.org>
Subject: Re: ports/91537: maths/xgobi - download site moved/maintainer addressupdate
Actually I need modify all my ports to use OptusNet rather than
Biolateral. Is there an easy way to do this or should I submit a
separate 1-line patch and PR for each port?
biology/crimap
biology/dna-qc
biology/flip
biology/primer3
biology/seqio
biology/wise
math/xgobi
net/generic-nqs
Submitted by: Tony Maher <anthony.maher@uts.edu.au>
L-Breeder is currently marked unfetchable:
http://people.freebsd.org/~fenner/portsurvey/biology.html#L-Breeder
So I tried to investigate the problem and I'm now submitting
my homework so it doesn't get lost.
This is what I noticed:
i) L-Breeder upstream sources have "stagnated for some time,
but now a new simplified version is available" (sic, from
the web site)
So, the fetch issue is resolved. And the pkg-descr is also
updated to reflect the new home page. However:
ii) L-Breeder is now called LBreeder. I have changed PORTNAME
to reflect this, although I don't know if this is the right
thing to do. Should the port be moved to biology/LBreeder?
Or perhaps just leaving PORTNAME pointing to the old name
and then work inside the Makefile to point the build/install
to the correct name?
iii) the sources have been reorganized so I have to update
the port's Makefile to reflect this. The attached patch
works for me under FreeBSD-4.11 (although it's possible
that I may have missed a dependency if I already have a
required library installed in my box. Sorry, I don't have
a tinderbox-like setup to test builds)
iv) the program does not have a version number, nor did I
find one by looking inside the sources. To avoid changing
too much the port I just left PORTVERSION at 1.0 and bumped
PORTREVISION to 6
Finally, do note that I am not a user of LBreeder, so I
cannot test the program myself. I just noticed that by
calling the executable I get a black X screen, that I can
quit by pressing 'q' as documented in Readme.txt, but I
can't tell myself if this is the expected behaviour. Nor
do I know how to use the example files. Caveat emptor.
PR: ports/90073
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
Approved by: maintainer timeout
This patch adds a LATEST_LINK line in the Makefile to avoid
duplication with the 'p5-bioperl' port in the packages/Latest
directory.
PR: ports/89916
Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net>
