Attachment #90495 for bug #127683

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#

PORTNAME=	paml
PORTVERSION=	4.1
CATEGORIES=	biology
MASTER_SITES=	http://abacus.gene.ucl.ac.uk/software/
DISTNAME=	${PORTNAME}${PORTVERSION}

MAINTAINER=	wenheping@gmail.com
COMMENT=	Phylogenetic Analysis by Maximum Likelihood (PAML)

USE_GMAKE=	YES
WRKSRC=		${WRKDIR}/${DISTNAME:S/.//g}/src
MAKE_ARGS=	CC="${CC}" CFLAGS="${CFLAGS}"

BINARIES=	baseml basemlg chi2 codeml evolver pamp yn00
DOC_FILES=	MCMCtreeDoc.pdf pamlDOC.pdf pamlFAQs.pdf pamlHistory.txt

do-install:
.for f in ${BINARIES}

.endfor
.if !defined(NOPORTDOCS)
	${MKDIR} ${DOCSDIR}
.for f in ${DOC_FILES}
	${INSTALL_DATA} ${WRKDIR}/${DISTNAME:S/.//g}/doc/${f} ${DOCSDIR}
.endfor
.endif

.include <bsd.port.mk>

Lines 1-3 Link Here

(-)distinfo (-3 / +3 lines)
1	MD5 (paml3.15.tar.gz) = c54ba7e15a66b57dc1140feea22e5695	1	MD5 (paml4.1.tar.gz) = df8d8a790f5ef29e7266640d4493ec1d
2	SHA256 (paml3.15.tar.gz) = f698b1d57b514e5e06e746899eae1245d098e96881e2a31c9b8fc956beb4f62a	2	SHA256 (paml4.1.tar.gz) = 64680a56304bb3f5cd61cfc9be253fe1fe37250cb450bceaaf76b99ee08111f1
3	SIZE (paml3.15.tar.gz) = 2364043	3	SIZE (paml4.1.tar.gz) = 2865301

Lines 7-10 Link Here

(-)pkg-plist (+3 lines)
7	bin/pamp	7	bin/pamp
8	bin/yn00	8	bin/yn00
9	%%PORTDOCS%%%%DOCSDIR%%/pamlDOC.pdf	9	%%PORTDOCS%%%%DOCSDIR%%/pamlDOC.pdf
		10	%%PORTDOCS%%%%DOCSDIR%%/MCMCtreeDoc.pdf
		11	%%PORTDOCS%%%%DOCSDIR%%/pamlFAQs.pdf
		12	%%PORTDOCS%%%%DOCSDIR%%/pamlHistory.txt
10	%%PORTDOCS%%@dirrm %%DOCSDIR%%	13	%%PORTDOCS%%@dirrm %%DOCSDIR%%

Return to bug 127683

Lines 6-24 Link Here

(-)Makefile (-5 / +7 lines)
6	#	6	#
7		7
8	PORTNAME= paml	8	PORTNAME= paml
9	PORTVERSION= 3.15	9	PORTVERSION= 4.1
10	CATEGORIES= biology	10	CATEGORIES= biology
11	MASTER_SITES= http://abacus.gene.ucl.ac.uk/software/	11	MASTER_SITES= http://abacus.gene.ucl.ac.uk/software/
12	DISTNAME= ${PORTNAME}${PORTVERSION}	12	DISTNAME= ${PORTNAME}${PORTVERSION}
13		13
14	MAINTAINER= ports@FreeBSD.org	14	MAINTAINER= wenheping@gmail.com
15	COMMENT= Phylogenetic Analysis by Maximum Likelihood (PAML)	15	COMMENT= Phylogenetic Analysis by Maximum Likelihood (PAML)
16		16
17	USE_GMAKE= YES	17	USE_GMAKE= YES
18	WRKSRC= ${WRKDIR}/${DISTNAME:S/b//g}/src	18	WRKSRC= ${WRKDIR}/${DISTNAME:S/.//g}/src
19	MAKE_ARGS= CC="${CC}" CFLAGS="${CFLAGS}"	19	MAKE_ARGS= CC="${CC}" CFLAGS="${CFLAGS}"
20		20
21	BINARIES= baseml basemlg chi2 codeml evolver pamp yn00	21	BINARIES= baseml basemlg chi2 codeml evolver pamp yn00
		22	DOC_FILES= MCMCtreeDoc.pdf pamlDOC.pdf pamlFAQs.pdf pamlHistory.txt
22		23
23	do-install:	24	do-install:
24	.for f in ${BINARIES}	25	.for f in ${BINARIES}
Lines 26-33 Link Here
26	.endfor	27	.endfor
27	.if !defined(NOPORTDOCS)	28	.if !defined(NOPORTDOCS)
28	${MKDIR} ${DOCSDIR}	29	${MKDIR} ${DOCSDIR}
29	${INSTALL_DATA} ${WRKDIR}/${DISTNAME:S/b//g}/doc/pamlDOC.pdf \	30	.for f in ${DOC_FILES}
30	${DOCSDIR}	31	${INSTALL_DATA} ${WRKDIR}/${DISTNAME:S/.//g}/doc/${f} ${DOCSDIR}
		32	.endfor
31	.endif	33	.endif
32		34
33	.include <bsd.port.mk>	35	.include <bsd.port.mk>