Attachment 146324 Details for Bug 193026 – biology_crux.diff

[patch] biology_crux.diff

biology_crux.diff (text/plain), 6.51 KB, created by tkato432 on 2014-08-26 18:31:35 UTC

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Creator: tkato432

Created: 2014-08-26 18:31:35 UTC

Size: 6.51 KB

patch

obsolete

>diff -urN /usr/ports/biology/crux/Makefile biology/crux/Makefile
>--- /usr/ports/biology/crux/Makefile	2014-07-30 03:54:15.000000000 +0900
>+++ biology/crux/Makefile	2014-08-27 00:00:00.000000000 +0900
>@@ -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 <bsd.port.options.mk>
> 
>-.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 <bsd.port.mk>
>diff -urN /usr/ports/biology/crux/pkg-descr biology/crux/pkg-descr
>--- /usr/ports/biology/crux/pkg-descr	2014-06-21 17:47:34.000000000 +0900
>+++ biology/crux/pkg-descr	2014-08-27 00:00:00.000000000 +0900
>@@ -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/
>diff -urN /usr/ports/biology/crux/pkg-install biology/crux/pkg-install
>--- /usr/ports/biology/crux/pkg-install	1970-01-01 09:00:00.000000000 +0900
>+++ biology/crux/pkg-install	2014-08-27 00:00:00.000000000 +0900
>@@ -0,0 +1,8 @@
>+#!/bin/sh
>+
>+case $2 in
>+POST-INSTALL)
>+	${PKG_PREFIX}/bin/crux -b -q /dev/null
>+	exit 0
>+	;;
>+esac
>diff -urN /usr/ports/biology/crux/pkg-plist biology/crux/pkg-plist
>--- /usr/ports/biology/crux/pkg-plist	2014-06-21 17:47:34.000000000 +0900
>+++ biology/crux/pkg-plist	2014-08-27 00:00:00.000000000 +0900
>@@ -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 @@
> %%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

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Attachments on bug 193026: 146324