Add the biology/crux port.

svn path=/head/; revision=235460

biology/Makefile

@@ -19,6 +19,7 @@
     SUBDIR += clustalw
     SUBDIR += consed
     SUBDIR += crimap
+    SUBDIR += crux
     SUBDIR += distribfold
     SUBDIR += dna-qc
     SUBDIR += dotter

biology/crux/Makefile

@@ -0,0 +1,38 @@
+# New ports collection makefile for:   crux
+# Date created:        8 June 2009
+# Whom:                jasone
+#
+# $FreeBSD$
+#
+
+PORTNAME=      crux
+PORTVERSION=   1.0.1
+CATEGORIES=    python biology
+MASTER_SITES=  http://www.canonware.com/download/Crux/
+
+MAINTAINER=    jasone@FreeBSD.org
+COMMENT=       Software toolkit for phylogenetic inference
+
+USE_BZIP2=     yes
+GNU_CONFIGURE= yes
+CONFIGURE_ARGS=--with-python=${PYTHON_CMD} --disable-mpi
+CONFIGURE_ENV+=EXTRA_CFLAGS="-std=gnu99"
+USE_GMAKE=     yes
+USE_PYTHON=    2.5+
+
+OPTIONS=       SYS_LINALG "Enable system ATLAS/LAPACK" Off
+
+.include <bsd.port.pre.mk>
+
+.if defined(WITH_SYS_LINALG)
+CONFIGURE_ARGS+= --enable-sys-linalg
+RUN_DEPENDS+=  libatlas:${PORTSDIR}/math/atlas
+.else
+CONFIGURE_ARGS+= --disable-sys-linalg
+USE_FORTRAN=   yes
+.endif
+
+post-install:
+	@${PREFIX}/bin/crux -b -q /dev/null
+
+.include <bsd.port.post.mk>

biology/crux/distinfo

@@ -0,0 +1,3 @@
+MD5 (crux-1.0.1.tar.bz2) = 782c27c686112f22f2808e7a99945ad7
+SHA256 (crux-1.0.1.tar.bz2) = de16b3a43d7b695b8b227fbefae87477d91c0f9a8a7695eacc453b3511256417
+SIZE (crux-1.0.1.tar.bz2) = 1169772

biology/crux/pkg-descr

@@ -0,0 +1,18 @@
+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/

biology/crux/pkg-plist

@@ -0,0 +1,71 @@
+@comment $FreeBSD$
+bin/crux
+bin/redpoint
+bin/MrRogers
+%%PYTHON_SITELIBDIR%%/Crux/__init__.py
+%%PYTHON_SITELIBDIR%%/Crux/__init__.so
+%%PYTHON_SITELIBDIR%%/Crux/Character.so
+%%PYTHON_SITELIBDIR%%/Crux/Config.py
+%%PYTHON_SITELIBDIR%%/Crux/Config.pyo
+%%PYTHON_SITELIBDIR%%/Crux/Copying.py
+%%PYTHON_SITELIBDIR%%/Crux/Copying.pyo
+%%PYTHON_SITELIBDIR%%/Crux/CTMatrix.so
+%%PYTHON_SITELIBDIR%%/Crux/DistMatrix/__init__.py
+%%PYTHON_SITELIBDIR%%/Crux/DistMatrix/__init__.so
+%%PYTHON_SITELIBDIR%%/Crux/DistMatrix/Nj.so
+%%PYTHON_SITELIBDIR%%/Crux/Fasta.so
+%%PYTHON_SITELIBDIR%%/Crux/Mc3/__init__.py
+%%PYTHON_SITELIBDIR%%/Crux/Mc3/__init__.so
+%%PYTHON_SITELIBDIR%%/Crux/Mc3/Chain.so
+%%PYTHON_SITELIBDIR%%/Crux/Mc3/Post.so
+%%PYTHON_SITELIBDIR%%/Crux/Newick.so
+%%PYTHON_SITELIBDIR%%/Crux/Taxa.so
+%%PYTHON_SITELIBDIR%%/Crux/Tree/__init__.py
+%%PYTHON_SITELIBDIR%%/Crux/Tree/__init__.so
+%%PYTHON_SITELIBDIR%%/Crux/Tree/Bipart.so
+%%PYTHON_SITELIBDIR%%/Crux/Tree/Lik.so
+%%PYTHON_SITELIBDIR%%/Crux/Tree/Sumt.so
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/__init__.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Character.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/CTMatrix.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Cx.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/CxMath.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/CxMat.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/CxNewickLexer.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/CxRi.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/DistMatrix/__init__.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/DistMatrix/CxDistMatrixLexer.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/DistMatrix/Nj.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Fasta.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3/__init__.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3/Chain.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3/Post.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Newick.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/SFMT/SFMT.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Taxa.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/__init__.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/Bipart.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/CxLik.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/Lik.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/Sumt.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/libm.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/libc.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Parsing.pxd
+share/Crux/lib/libCx.so
+share/Crux/parsers/Fasta.log
+share/Crux/parsers/Fasta.pickle
+share/Crux/parsers/Newick.log
+share/Crux/parsers/Newick.pickle
+@dirrm %%PYTHON_SITELIBDIR%%/Crux/DistMatrix
+@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/DistMatrix
+@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3
+@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/SFMT
+@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree
+@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux
+@dirrm %%PYTHON_SITELIBDIR%%/Crux/include
+@dirrm %%PYTHON_SITELIBDIR%%/Crux/Mc3
+@dirrm %%PYTHON_SITELIBDIR%%/Crux/Tree
+@dirrm %%PYTHON_SITELIBDIR%%/Crux
+@dirrm share/Crux/lib
+@dirrm share/Crux/parsers
+@dirrm share/Crux