freebsd-ports/biology/paml/Makefile

# Created by: dbader@eece.unm.edu
# $FreeBSD$

PORTNAME=	paml
PORTVERSION=	4.8a
CATEGORIES=	biology
MASTER_SITES=	http://abacus.gene.ucl.ac.uk/software/
DISTNAME=	${PORTNAME}${PORTVERSION}

MAINTAINER=	jrm@ftfl.ca
COMMENT=	Phylogenetic Analysis by Maximum Likelihood (PAML)

USES=		gmake tar:tgz
WRKSRC=		${WRKDIR}/${PORTNAME}4.8/src
MAKE_ARGS=	CC="${CC}" CFLAGS="${CFLAGS}"

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

OPTIONS_DEFINE=	DOCS

do-install:
.for f in ${BINARIES}
	${INSTALL_PROGRAM} ${WRKSRC}/${f} ${STAGEDIR}${PREFIX}/bin
.endfor
	@${MKDIR} ${STAGEDIR}${DOCSDIR}
.for f in ${DOC_FILES}
	${INSTALL_DATA} ${WRKSRC}/../doc/${f} ${STAGEDIR}${DOCSDIR}
.endfor

.include <bsd.port.mk>
- Trim Makefile headers 2013-06-01 16:22:35 +02:00			`# Created by: dbader@eece.unm.edu`
Add paml version 3.01. A set of utilities for performing Phylogenetic Analysis by Maximum Likelihood (PAML). PR: 19753 Submitted by: David A. Bader <dbader@cielo.eece.unm.edu> 2000-07-10 05:21:05 +02:00			`# $FreeBSD$`

			`PORTNAME= paml`
Update biology/paml to 4.8a and unbreak. PR: 199264 Submitted by: Joseph Mingrone <jrm@ftfl.ca> Approved by: bdrewery (mentor) 2015-04-10 17:39:01 +02:00			`PORTVERSION= 4.8a`
Add paml version 3.01. A set of utilities for performing Phylogenetic Analysis by Maximum Likelihood (PAML). PR: 19753 Submitted by: David A. Bader <dbader@cielo.eece.unm.edu> 2000-07-10 05:21:05 +02:00			`CATEGORIES= biology`
Update to 3.14b Update MASTER_SITES Add SHA256 Remove extra TABS PR: 88007 Submitted by: Jean Milanez Melo <jmelo@freebsdbrasil.com.br> Approved by: maintainer timeout, 14 days 2005-11-10 02:21:42 +01:00			`MASTER_SITES= http://abacus.gene.ucl.ac.uk/software/`
* Update to 3.13. PR: 48255 Submitted by: David A. Bader <dbader@eece.unm.edu> * Also honor CC/CFLAGS. 2003-02-15 00:21:23 +01:00			`DISTNAME= ${PORTNAME}${PORTVERSION}`
Add paml version 3.01. A set of utilities for performing Phylogenetic Analysis by Maximum Likelihood (PAML). PR: 19753 Submitted by: David A. Bader <dbader@cielo.eece.unm.edu> 2000-07-10 05:21:05 +02:00
- Pass maintainership to submitter PR: 196859 Submitted by: Joseph Mingrone<jrm@ftfl.ca> 2015-01-19 13:11:25 +01:00			`MAINTAINER= jrm@ftfl.ca`
* Update to 3.13. PR: 48255 Submitted by: David A. Bader <dbader@eece.unm.edu> * Also honor CC/CFLAGS. 2003-02-15 00:21:23 +01:00			`COMMENT= Phylogenetic Analysis by Maximum Likelihood (PAML)`
Add paml version 3.01. A set of utilities for performing Phylogenetic Analysis by Maximum Likelihood (PAML). PR: 19753 Submitted by: David A. Bader <dbader@cielo.eece.unm.edu> 2000-07-10 05:21:05 +02:00
Convert a bunch of EXTRACT_SUFX=... into USES=tar:... Approved by: portmgr (not really, but touches unstaged ports) 2014-07-29 21:11:51 +02:00			`USES= gmake tar:tgz`
Update biology/paml to 4.8a and unbreak. PR: 199264 Submitted by: Joseph Mingrone <jrm@ftfl.ca> Approved by: bdrewery (mentor) 2015-04-10 17:39:01 +02:00			`WRKSRC= ${WRKDIR}/${PORTNAME}4.8/src`
* Update to 3.13. PR: 48255 Submitted by: David A. Bader <dbader@eece.unm.edu> * Also honor CC/CFLAGS. 2003-02-15 00:21:23 +01:00			`MAKE_ARGS= CC="${CC}" CFLAGS="${CFLAGS}"`
Add paml version 3.01. A set of utilities for performing Phylogenetic Analysis by Maximum Likelihood (PAML). PR: 19753 Submitted by: David A. Bader <dbader@cielo.eece.unm.edu> 2000-07-10 05:21:05 +02:00
Update to 3.14 PR: ports/72422 Submitted by: Choe, Cheng-Dae <whitekid@gmail.com> 2004-11-06 04:55:37 +01:00			`BINARIES= baseml basemlg chi2 codeml evolver pamp yn00`
- Update to 4.8 - Reset maintainer to ports@ 2014-04-05 12:56:52 +02:00			`DOC_FILES= pamlDOC.pdf pamlFAQs.pdf pamlHistory.txt`
Add paml version 3.01. A set of utilities for performing Phylogenetic Analysis by Maximum Likelihood (PAML). PR: 19753 Submitted by: David A. Bader <dbader@cielo.eece.unm.edu> 2000-07-10 05:21:05 +02:00
Remove trailing whitespaces from category biology 2014-02-21 14:35:26 +01:00			`OPTIONS_DEFINE= DOCS`
According to the Porter's Handbook (5.12.2.3.) default options must be added to OPTIONS_DEFINE. This policy has been implemented only recently that's why we have many ports violating this policy. This patch adds the default options specified in the Porter's Handbook to OPTIONS_DEFINE where they are being used. Ports maintained by gnome@FreeBSD.org, kde@FreeBSD.org and x11@FreeBSD.org have been excluded. Approved by: portmgr (bapt) 2014-02-10 14:54:26 +01:00
Add paml version 3.01. A set of utilities for performing Phylogenetic Analysis by Maximum Likelihood (PAML). PR: 19753 Submitted by: David A. Bader <dbader@cielo.eece.unm.edu> 2000-07-10 05:21:05 +02:00			`do-install:`
			`.for f in ${BINARIES}`
Support staging 2014-03-14 13:59:33 +01:00			`${INSTALL_PROGRAM} ${WRKSRC}/${f} ${STAGEDIR}${PREFIX}/bin`
Add paml version 3.01. A set of utilities for performing Phylogenetic Analysis by Maximum Likelihood (PAML). PR: 19753 Submitted by: David A. Bader <dbader@cielo.eece.unm.edu> 2000-07-10 05:21:05 +02:00			`.endfor`
Support staging 2014-03-14 13:59:33 +01:00			`@${MKDIR} ${STAGEDIR}${DOCSDIR}`
- Update to 4.1 - Pass maintainership to submitter PR: 127683 Submitted by: Wen heping <wenheping@gmail.com> 2008-09-30 10:54:55 +02:00			`.for f in ${DOC_FILES}`
Update biology/paml to 4.8a and unbreak. PR: 199264 Submitted by: Joseph Mingrone <jrm@ftfl.ca> Approved by: bdrewery (mentor) 2015-04-10 17:39:01 +02:00			`${INSTALL_DATA} ${WRKSRC}/../doc/${f} ${STAGEDIR}${DOCSDIR}`
- Update to 4.1 - Pass maintainership to submitter PR: 127683 Submitted by: Wen heping <wenheping@gmail.com> 2008-09-30 10:54:55 +02:00			`.endfor`
Add paml version 3.01. A set of utilities for performing Phylogenetic Analysis by Maximum Likelihood (PAML). PR: 19753 Submitted by: David A. Bader <dbader@cielo.eece.unm.edu> 2000-07-10 05:21:05 +02:00
			`.include <bsd.port.mk>`