diff options
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/crux/Makefile | 38 | ||||
| -rw-r--r-- | biology/crux/distinfo | 3 | ||||
| -rw-r--r-- | biology/crux/pkg-descr | 18 | ||||
| -rw-r--r-- | biology/crux/pkg-plist | 71 |
5 files changed, 131 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index 8f120d02a7b3..20a3d819973d 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -19,6 +19,7 @@ SUBDIR += clustalw SUBDIR += consed SUBDIR += crimap + SUBDIR += crux SUBDIR += distribfold SUBDIR += dna-qc SUBDIR += dotter diff --git a/biology/crux/Makefile b/biology/crux/Makefile new file mode 100644 index 000000000000..fc9b8c38ae2d --- /dev/null +++ b/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> diff --git a/biology/crux/distinfo b/biology/crux/distinfo new file mode 100644 index 000000000000..da851ea3cc85 --- /dev/null +++ b/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 diff --git a/biology/crux/pkg-descr b/biology/crux/pkg-descr new file mode 100644 index 000000000000..044b39424386 --- /dev/null +++ b/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/ diff --git a/biology/crux/pkg-plist b/biology/crux/pkg-plist new file mode 100644 index 000000000000..a7e4291e4b56 --- /dev/null +++ b/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 |