Attachment #146324 for bug #193026

View | Details | Raw Unified | Return to bug 193026
Collapse All | Expand All





PORTNAME=	crux
PORTVERSION=	1.2.0
PORTREVISION=	4
CATEGORIES=	biology python
MASTER_SITES=	http://www.canonware.com/download/Crux/

MAINTAINER=	ports@FreeBSD.org
COMMENT=	Software toolkit for phylogenetic inference

LICENSE=	BSD2CLAUSE BSD3CLAUSE
LICENSE_COMB=	multi
CONFIGURE_ARGS=	--with-python=${PYTHON_CMD} --disable-mpi
USE_CSTD=	gnu99
USE_PYTHON=	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 ${OSVERSION} > 900000
BROKEN_powerpc=	Does not build on powerpc-9: error in pthreads
LIB_DEPENDS+=	libatlas.so:${PORTSDIR}/math/atlas
.else
CONFIGURE_ARGS+=	--disable-sys-linalg
.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:
	@(${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>




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/

Line 0 Link Here

(-)biology/crux/pkg-install (+8 lines)
	1	#!/bin/sh
	2
	3	case $2 in
	4	POST-INSTALL)
	5	${PKG_PREFIX}/bin/crux -b -q /dev/null
	6	exit 0
	7	;;
	8	esac




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
@rmtry %%PYTHON_SITELIBDIR%%/Crux/Config.pyo
%%PYTHON_SITELIBDIR%%/Crux/Copying.py
@rmtry %%PYTHON_SITELIBDIR%%/Crux/Copying.pyo
%%PYTHON_SITELIBDIR%%/Crux/DistMatrix/Nj.so
%%PYTHON_SITELIBDIR%%/Crux/DistMatrix/__init__.py
%%PYTHON_SITELIBDIR%%/Crux/DistMatrix/__init__.so

%%PYTHON_SITELIBDIR%%/Crux/__init__.py
%%PYTHON_SITELIBDIR%%/Crux/__init__.so
%%PYTHON_SITELIBDIR%%/Parsing.so
@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 lib/Crux/parsers
@dirrm lib/Crux/lib
@dirrm lib/Crux

Return to bug 193026

Lines 3-43 Link Here

(-)biology/crux/Makefile (-19 / +27 lines)
3		3
4	PORTNAME= crux	4	PORTNAME= crux
5	PORTVERSION= 1.2.0	5	PORTVERSION= 1.2.0
6	PORTREVISION= 3	6	PORTREVISION= 4
7	CATEGORIES= biology python	7	CATEGORIES= biology python
8	MASTER_SITES= http://www.canonware.com/download/Crux/	8	MASTER_SITES= http://www.canonware.com/download/Crux/
9		9
10	MAINTAINER= ports@FreeBSD.org	10	MAINTAINER= ports@FreeBSD.org
11	COMMENT= Software toolkit for phylogenetic inference	11	COMMENT= Software toolkit for phylogenetic inference
12		12
13	USES= fortran gmake tar:bzip2	13	LICENSE= BSD2CLAUSE BSD3CLAUSE
14	GNU_CONFIGURE= yes	14	LICENSE_COMB= multi
15	CONFIGURE_ARGS= --with-python=${PYTHON_CMD} --disable-mpi
16	USE_CSTD= gnu99
17	USE_PYTHON= yes
18		15
19	OPTIONS_DEFINE= SYS_LINALG	16	USES= fortran gmake python tar:bzip2
20	SYS_LINALG_DESC= Enable system ATLAS/LAPACK	17	USE_CSTD= gnu99
21		18	GNU_CONFIGURE= yes
22	NO_STAGE= yes	19	CONFIGURE_ARGS= --datadir=${PREFIX}/lib \
		20	--with-python=${PYTHON_CMD} \
		21	--disable-mpi
23		22
24	CPPFLAGS+= -I${LOCALBASE}/include	23	CPPFLAGS+= -I${LOCALBASE}/include
25	LDFLAGS+= -L${LOCALBASE}/lib	24	LDFLAGS+= -L${LOCALBASE}/lib
26		25
		26	OPTIONS_DEFINE= SYS_LINALG
		27	SYS_LINALG_DESC= Enable system ATLAS/LAPACK
		28	SYS_LINALG_LIB_DEPENDS= libatlas.so:${PORTSDIR}/math/atlas
		29	SYS_LINALG_CONFIGURE_ENABLE= sys-linalg
		30
27	.include <bsd.port.options.mk>	31	.include <bsd.port.options.mk>
28		32
29	.if ${PORT_OPTIONS:MSYS_LINALG}	33	.if ${OSVERSION} > 900000
30	CONFIGURE_ARGS+= --enable-sys-linalg	34	BROKEN_powerpc= Does not build on powerpc-9: error in pthreads
31	LIB_DEPENDS+= libatlas.so:${PORTSDIR}/math/atlas
32	.else
33	CONFIGURE_ARGS+= --disable-sys-linalg
34	.endif	35	.endif
35		36
36	.if ${ARCH} == "powerpc" && ${OSVERSION} > 900000	37	post-patch:
37	BROKEN= Does not build on powerpc-9: error in pthreads	38	@${REINPLACE_CMD} -e \
38	.endif	39	's\|\([[:blank:]]\)\($$(BINDIR)\)\|\1$$(DESTDIR)\2\| ; \
		40	s\|\([[:blank:]]\)\($$(DATADIR)\)\|\1$$(DESTDIR)\2\| ; \
		41	s\|\(,\)\(@site_packages@\)\|\1$$(DESTDIR)\2\| ; \
		42	s\|\([[:blank:]]\)\(@site_packages@\)\|\1$$(DESTDIR)\2\|' \
		43	${WRKSRC}/Makefile.in
39		44
40	post-install:	45	post-install:
41	@${PREFIX}/bin/crux -b -q /dev/null	46	@(${FIND} ${STAGEDIR}${PREFIX}/lib/Crux/lib -maxdepth 1 -type f \
		47	-name "*.so" \| ${XARGS} ${STRIP_CMD})
		48	@(${FIND} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} -maxdepth 3 -type f \
		49	-name "*.so" \| ${XARGS} ${STRIP_CMD})
42		50
43	.include <bsd.port.mk>	51	.include <bsd.port.mk>

Lines 1-18 Link Here

(-)biology/crux/pkg-descr (-13 / +14 lines)
1	Crux is a software toolkit for molecular phylogenetic inference. It is	1	Crux is a software toolkit for molecular phylogenetic inference. It is
2	structured as a set of Python modules, which makes it possible to quickly	2	structured as a set of Python modules, which makes it possible to quickly
3	develop Python scripts that perform unique, non-canned analyses. Features	3	develop Python scripts that perform unique, non-canned analyses. Features
4	include:	4	include:
5	* Tree log-likelihoods can be computed under a variety of models, including all	5	* Tree log-likelihoods can be computed under a variety of models,
6	specializations of GTR+I+G and mixture models. Tree likelihoods can be	6	including all specializations of GTR+I+G and mixture models. Tree
7	computed in parallel via pthreads.	7	likelihoods can be computed in parallel via pthreads.
8	* Bayesian Markov chain Monte Carlo (MCMC) methods (with Metropolis coupling)	8	* Bayesian Markov chain Monte Carlo (MCMC) methods (with Metropolis
9	can sample among non-nested models using reversible model jumps.	9	coupling) can sample among non-nested models using reversible model
10	* Crux is capable of simulating character data under any model its likelihood	10	jumps.
11	engine is capable of.	11	* Crux is capable of simulating character data under any model its
12	* The neighbor joining (NJ) and relaxed neighbor joining (RNJ) implementations	12	likelihood engine is capable of.
13	are among the fastest in existence.	13	* The neighbor joining (NJ) and relaxed neighbor joining (RNJ)
		14	implementations are among the fastest in existence.
14	* Pairwise distances between sequences can be computed based on percent	15	* Pairwise distances between sequences can be computed based on percent
15	identity, or using methods that correct for multiple hits (Jukes-Cantor,	16	identity, or using methods that correct for multiple hits
16	Kimura, and logDet).	17	(Jukes-Cantor, Kimura, and logDet).
17		18
18	WWW: http://www.canonware.com/Crux/	19	WWW: http://www.canonware.com/Crux/

Lines 1-12 Link Here

(-)biology/crux/pkg-plist (-14 / +14 lines)
1	bin/crux	1	bin/crux
2	bin/redpoint	2	bin/redpoint
3	bin/MrRogers	3	bin/MrRogers
		4	lib/Crux/lib/libCx.so
		5	lib/Crux/parsers/Fasta.log
		6	lib/Crux/parsers/Fasta.pickle
4	%%PYTHON_SITELIBDIR%%/Crux/CTMatrix.so	7	%%PYTHON_SITELIBDIR%%/Crux/CTMatrix.so
5	%%PYTHON_SITELIBDIR%%/Crux/Character.so	8	%%PYTHON_SITELIBDIR%%/Crux/Character.so
6	%%PYTHON_SITELIBDIR%%/Crux/Config.py	9	%%PYTHON_SITELIBDIR%%/Crux/Config.py
7	%%PYTHON_SITELIBDIR%%/Crux/Config.pyo	10	@rmtry %%PYTHON_SITELIBDIR%%/Crux/Config.pyo
8	%%PYTHON_SITELIBDIR%%/Crux/Copying.py	11	%%PYTHON_SITELIBDIR%%/Crux/Copying.py
9	%%PYTHON_SITELIBDIR%%/Crux/Copying.pyo	12	@rmtry %%PYTHON_SITELIBDIR%%/Crux/Copying.pyo
10	%%PYTHON_SITELIBDIR%%/Crux/DistMatrix/Nj.so	13	%%PYTHON_SITELIBDIR%%/Crux/DistMatrix/Nj.so
11	%%PYTHON_SITELIBDIR%%/Crux/DistMatrix/__init__.py	14	%%PYTHON_SITELIBDIR%%/Crux/DistMatrix/__init__.py
12	%%PYTHON_SITELIBDIR%%/Crux/DistMatrix/__init__.so	15	%%PYTHON_SITELIBDIR%%/Crux/DistMatrix/__init__.so
Lines 51-72 Link Here
51	%%PYTHON_SITELIBDIR%%/Crux/__init__.py	54	%%PYTHON_SITELIBDIR%%/Crux/__init__.py
52	%%PYTHON_SITELIBDIR%%/Crux/__init__.so	55	%%PYTHON_SITELIBDIR%%/Crux/__init__.so
53	%%PYTHON_SITELIBDIR%%/Parsing.so	56	%%PYTHON_SITELIBDIR%%/Parsing.so
54	share/Crux/lib/libCx.so	57	@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree
55	share/Crux/parsers/Fasta.log	58	@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/SFMT
56	share/Crux/parsers/Fasta.pickle	59	@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3
57	@dirrm %%PYTHON_SITELIBDIR%%/Crux/DistMatrix	60	@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/DistMatrix
58	@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/DistMatrix	61	@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/DistMatrix
59	@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/Tree	62	@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/Tree
60	@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux	63	@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux
61	@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/DistMatrix
62	@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3
63	@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/SFMT
64	@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree
65	@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux	64	@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux
66	@dirrm %%PYTHON_SITELIBDIR%%/Crux/include	65	@dirrm %%PYTHON_SITELIBDIR%%/Crux/include
67	@dirrm %%PYTHON_SITELIBDIR%%/Crux/Mc3
68	@dirrm %%PYTHON_SITELIBDIR%%/Crux/Tree	66	@dirrm %%PYTHON_SITELIBDIR%%/Crux/Tree
		67	@dirrm %%PYTHON_SITELIBDIR%%/Crux/Mc3
		68	@dirrm %%PYTHON_SITELIBDIR%%/Crux/DistMatrix
69	@dirrm %%PYTHON_SITELIBDIR%%/Crux	69	@dirrm %%PYTHON_SITELIBDIR%%/Crux
70	@dirrm share/Crux/lib	70	@dirrm lib/Crux/parsers
71	@dirrm share/Crux/parsers	71	@dirrm lib/Crux/lib
72	@dirrm share/Crux	72	@dirrm lib/Crux