From owner-svn-ports-head@FreeBSD.ORG Tue Aug 26 20:39:06 2014 Return-Path: Delivered-To: svn-ports-head@freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTPS id 467ED669; Tue, 26 Aug 2014 20:39:06 +0000 (UTC) Received: from svn.freebsd.org (svn.freebsd.org [IPv6:2001:1900:2254:2068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id 30F813AA6; Tue, 26 Aug 2014 20:39:06 +0000 (UTC) Received: from svn.freebsd.org ([127.0.1.70]) by svn.freebsd.org (8.14.9/8.14.9) with ESMTP id s7QKd6bU000363; Tue, 26 Aug 2014 20:39:06 GMT (envelope-from rene@FreeBSD.org) Received: (from rene@localhost) by svn.freebsd.org (8.14.9/8.14.9/Submit) id s7QKd5v5000359; Tue, 26 Aug 2014 20:39:05 GMT (envelope-from rene@FreeBSD.org) Message-Id: <201408262039.s7QKd5v5000359@svn.freebsd.org> X-Authentication-Warning: svn.freebsd.org: rene set sender to rene@FreeBSD.org using -f From: Rene Ladan Date: Tue, 26 Aug 2014 20:39:05 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r366266 - in head/biology/crux: . files X-SVN-Group: ports-head MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.18-1 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 26 Aug 2014 20:39:06 -0000 Author: rene Date: Tue Aug 26 20:39:05 2014 New Revision: 366266 URL: http://svnweb.freebsd.org/changeset/ports/366266 QAT: https://qat.redports.org/buildarchive/r366266/ Log: biology/crux: stage, modernize, add license (BSD[23]CLAUSE), cleanups PR: 193026 Submitted by: Ports Fury Added: head/biology/crux/files/ head/biology/crux/files/pkg-install (contents, props changed) Modified: head/biology/crux/Makefile head/biology/crux/pkg-descr head/biology/crux/pkg-plist Modified: head/biology/crux/Makefile ============================================================================== --- head/biology/crux/Makefile Tue Aug 26 20:35:42 2014 (r366265) +++ head/biology/crux/Makefile Tue Aug 26 20:39:05 2014 (r366266) @@ -3,41 +3,49 @@ PORTNAME= crux PORTVERSION= 1.2.0 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= biology python MASTER_SITES= http://www.canonware.com/download/Crux/ MAINTAINER= ports@FreeBSD.org COMMENT= Software toolkit for phylogenetic inference -USES= fortran gmake tar:bzip2 -GNU_CONFIGURE= yes -CONFIGURE_ARGS= --with-python=${PYTHON_CMD} --disable-mpi -USE_CSTD= gnu99 -USE_PYTHON= yes +LICENSE= BSD2CLAUSE BSD3CLAUSE +LICENSE_COMB= multi -OPTIONS_DEFINE= SYS_LINALG -SYS_LINALG_DESC= Enable system ATLAS/LAPACK - -NO_STAGE= yes +USES= fortran gmake python tar:bzip2 +USE_CSTD= gnu99 +GNU_CONFIGURE= yes +CONFIGURE_ARGS= --datadir=${PREFIX}/lib \ + --with-python=${PYTHON_CMD} \ + --disable-mpi CPPFLAGS+= -I${LOCALBASE}/include LDFLAGS+= -L${LOCALBASE}/lib +OPTIONS_DEFINE= SYS_LINALG +SYS_LINALG_DESC= Enable system ATLAS/LAPACK +SYS_LINALG_LIB_DEPENDS= libatlas.so:${PORTSDIR}/math/atlas +SYS_LINALG_CONFIGURE_ENABLE= sys-linalg + .include -.if ${PORT_OPTIONS:MSYS_LINALG} -CONFIGURE_ARGS+= --enable-sys-linalg -LIB_DEPENDS+= libatlas.so:${PORTSDIR}/math/atlas -.else -CONFIGURE_ARGS+= --disable-sys-linalg +.if ${OSVERSION} > 900000 +BROKEN_powerpc= Does not build on powerpc-9: error in pthreads .endif -.if ${ARCH} == "powerpc" && ${OSVERSION} > 900000 -BROKEN= Does not build on powerpc-9: error in pthreads -.endif +post-patch: + @${REINPLACE_CMD} -e \ + 's|\([[:blank:]]\)\($$(BINDIR)\)|\1$$(DESTDIR)\2| ; \ + s|\([[:blank:]]\)\($$(DATADIR)\)|\1$$(DESTDIR)\2| ; \ + s|\(,\)\(@site_packages@\)|\1$$(DESTDIR)\2| ; \ + s|\([[:blank:]]\)\(@site_packages@\)|\1$$(DESTDIR)\2|' \ + ${WRKSRC}/Makefile.in post-install: - @${PREFIX}/bin/crux -b -q /dev/null + @(${FIND} ${STAGEDIR}${PREFIX}/lib/Crux/lib -maxdepth 1 -type f \ + -name "*.so" | ${XARGS} ${STRIP_CMD}) + @(${FIND} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} -maxdepth 3 -type f \ + -name "*.so" | ${XARGS} ${STRIP_CMD}) .include Added: head/biology/crux/files/pkg-install ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/crux/files/pkg-install Tue Aug 26 20:39:05 2014 (r366266) @@ -0,0 +1,8 @@ +#!/bin/sh + +case $2 in +POST-INSTALL) + ${PKG_PREFIX}/bin/crux -b -q /dev/null + exit 0 + ;; +esac Modified: head/biology/crux/pkg-descr ============================================================================== --- head/biology/crux/pkg-descr Tue Aug 26 20:35:42 2014 (r366265) +++ head/biology/crux/pkg-descr Tue Aug 26 20:39:05 2014 (r366266) @@ -1,18 +1,19 @@ -Crux is a software toolkit for molecular phylogenetic inference. It is +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 +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. +* 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). + identity, or using methods that correct for multiple hits + (Jukes-Cantor, Kimura, and logDet). WWW: http://www.canonware.com/Crux/ Modified: head/biology/crux/pkg-plist ============================================================================== --- head/biology/crux/pkg-plist Tue Aug 26 20:35:42 2014 (r366265) +++ head/biology/crux/pkg-plist Tue Aug 26 20:39:05 2014 (r366266) @@ -1,12 +1,15 @@ bin/crux bin/redpoint bin/MrRogers +lib/Crux/lib/libCx.so +lib/Crux/parsers/Fasta.log +lib/Crux/parsers/Fasta.pickle %%PYTHON_SITELIBDIR%%/Crux/CTMatrix.so %%PYTHON_SITELIBDIR%%/Crux/Character.so %%PYTHON_SITELIBDIR%%/Crux/Config.py -%%PYTHON_SITELIBDIR%%/Crux/Config.pyo +@rmtry %%PYTHON_SITELIBDIR%%/Crux/Config.pyo %%PYTHON_SITELIBDIR%%/Crux/Copying.py -%%PYTHON_SITELIBDIR%%/Crux/Copying.pyo +@rmtry %%PYTHON_SITELIBDIR%%/Crux/Copying.pyo %%PYTHON_SITELIBDIR%%/Crux/DistMatrix/Nj.so %%PYTHON_SITELIBDIR%%/Crux/DistMatrix/__init__.py %%PYTHON_SITELIBDIR%%/Crux/DistMatrix/__init__.so @@ -51,22 +54,19 @@ bin/MrRogers %%PYTHON_SITELIBDIR%%/Crux/__init__.py %%PYTHON_SITELIBDIR%%/Crux/__init__.so %%PYTHON_SITELIBDIR%%/Parsing.so -share/Crux/lib/libCx.so -share/Crux/parsers/Fasta.log -share/Crux/parsers/Fasta.pickle -@dirrm %%PYTHON_SITELIBDIR%%/Crux/DistMatrix +@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree +@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/SFMT +@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3 +@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/DistMatrix @dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/DistMatrix @dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/Tree @dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux -@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/Mc3 +@dirrm %%PYTHON_SITELIBDIR%%/Crux/DistMatrix @dirrm %%PYTHON_SITELIBDIR%%/Crux -@dirrm share/Crux/lib -@dirrm share/Crux/parsers -@dirrm share/Crux +@dirrm lib/Crux/parsers +@dirrm lib/Crux/lib +@dirrm lib/Crux