crux 1.2.0_1 biology =0

Software toolkit for phylogenetic inference
Maintained by: jasone@FreeBSD.org
Port Added: 08 Jun 2009 23:51:06
Also Listed In: python
License: not specified in port

Crux is a software toolkit for molecular phylogenetic inference.  It is
structured as a set of Python modules, which makes it possible to quickly
develop Python scripts that perform unique, non-canned analyses.  Features
include:
* Tree log-likelihoods can be computed under a variety of models, including all
  specializations of GTR+I+G and mixture models.  Tree likelihoods can be
  computed in parallel via pthreads.
* Bayesian Markov chain Monte Carlo (MCMC) methods (with Metropolis coupling)
  can sample among non-nested models using reversible model jumps.
* Crux is capable of simulating character data under any model its likelihood
  engine is capable of.
* The neighbor joining (NJ) and relaxed neighbor joining (RNJ) implementations
  are among the fastest in existence.
* Pairwise distances between sequences can be computed based on percent
  identity, or using methods that correct for multiple hits (Jukes-Cantor,
  Kimura, and logDet).

WWW: http://www.canonware.com/Crux/

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: lang/python27, devel/gmake, lang/gcc46, devel/binutils
Required To Run: lang/python27, lang/gcc46
There are no ports dependent upon this port

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

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Configuration Options

===> The following configuration options are available for crux-1.2.0_1:
     SYS_LINALG=Off (default) "Enable system ATLAS/LAPACK"
===> Use 'make config' to modify these settings

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Master Sites:

http://www.canonware.com/download/Crux/

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

Does not build on powerpc-9: error in pthreads.

Hat:            portmgr
Feature safe:   yes

- Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS)
- Fix all ports that add {CPP,LD}FLAGS to *_ENV to modify flags instead

PR:             157936
Submitted by:   myself
Exp-runs by:    pav
Approved by:    pav

- Get Rid MD5 support

Update to Crux 1.2.0.

Feature safe:   yes

Bump PORTREVISION for everything that sets USE_FORTRAN=yes which now
implies lang/gcc44 up from lang/gcc43.

Approved by:    portmgr

Fix PKGORIGIN

Submitted by:   pointyhat

Update to Crux 1.1.0.

Fix the ATLAS/LAPACK build option.

Change CONFIGURE_ENV --> USE_CSTD. [1]

Add missing pkg-plist entry for Parsing.so. [2]

Change RUN_DEPENDS --> LIB_DEPENDS for optional math/atlas dependency.

Submitted by:   [1] erwin
Reported by:    [2] QAT

Add the biology/crux port.

15 vulnerabilities affecting 34 ports have been reported in the past 14 days

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