ports/160083: Update port: biology/fastdnaml

[KATO Tsuguru]

>Number:         160083
>Category:       ports
>Synopsis:       Update port: biology/fastdnaml
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Wed Aug 24 18:50:15 UTC 2011
>Closed-Date:
>Last-Modified:
>Originator:     KATO Tsuguru
>Release:        FreeBSD 7.4-RELEASE-p2 i386
>Organization:
>Environment:
>Description:
- Fix MASTER_SITES and WWW: line
- Add LICENSE
- Support CC/CFLAGS properly

>How-To-Repeat:
>Fix:

diff -urN /usr/ports/biology/fastdnaml/Makefile biology/fastdnaml/Makefile
--- /usr/ports/biology/fastdnaml/Makefile	2011-08-02 15:46:34.000000000 +0900
+++ biology/fastdnaml/Makefile	2011-08-25 00:12:15.000000000 +0900
@@ -7,30 +7,28 @@
 
 PORTNAME=	fastdnaml
 PORTVERSION=	1.2.2
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	biology
-MASTER_SITES=	http://geta.life.uiuc.edu:80/~gary/programs/fastDNAml/
+MASTER_SITES=	http://www.life.illinois.edu/gary/programs/fastDNAml/
 DISTNAME=	fastDNAml_${PORTVERSION}
 
 MAINTAINER=	ports at FreeBSD.org
 COMMENT=	Faster DNAML, makes phylogenetic trees using maximum likelihood
 
-DEPRECATED=	No more public distfiles
-EXPIRATION_DATE=	2011-09-01
+LICENSE=	GPLv2 # (or later)
+LICENSE_FILE=	${WRKSRC}/GNU_GENERAL_PUBLIC_LICENSE
 
-USE_GMAKE=	yes
-do-build:
-	@(cd ${WRKSRC}/source; ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET})
+BUILD_WRKSRC=	${WRKSRC}/source
+
+MAKE_ARGS=	CC="${CC}" CFLAGS="${CFLAGS}"
 
 do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/source/fastDNAml ${PREFIX}/bin
-	${MKDIR} ${PREFIX}/bin/${PORTNAME}
+	${INSTALL_PROGRAM} ${BUILD_WRKSRC}/fastDNAml ${PREFIX}/bin
+	@${MKDIR} ${PREFIX}/bin/${PORTNAME}
 	${INSTALL_SCRIPT} ${WRKSRC}/scripts/* ${PREFIX}/bin/${PORTNAME}
-
-post-install:
 .if !defined(NOPORTDOCS)
-	${MKDIR} ${PREFIX}/share/doc/${PORTNAME}
-	${INSTALL_DATA} ${WRKSRC}/docs/*.txt ${PREFIX}/share/doc/${PORTNAME}
+	@${MKDIR} ${DOCSDIR}
+	${INSTALL_DATA} ${WRKSRC}/docs/*.txt ${DOCSDIR}
 .endif
 
 .include <bsd.port.mk>
diff -urN /usr/ports/biology/fastdnaml/pkg-descr biology/fastdnaml/pkg-descr
--- /usr/ports/biology/fastdnaml/pkg-descr	2000-10-12 21:31:13.000000000 +0900
+++ biology/fastdnaml/pkg-descr	2011-08-16 19:13:56.000000000 +0900
@@ -1,22 +1,10 @@
-fastDNAml is a program for estimating maximum likelihood phylogenetic trees
-from nucleotide sequences. 
+fastDNAml is a program derived from Joseph Felsenstein's version 3.3 DNAML
+(part of his PHYLIP package). Users should consult the documentation for
+DNAML before using this program.
+
+fastDNAml is an attempt to solve the same problem as DNAML, but to do so
+faster and using less memory, so that larger trees and/or more bootstrap
+replicates become tractable. Much of fastDNAml is merely a recoding of the
+PHYLIP 3.3 DNAML program from PASCAL to C.
 
-WWW: http://geta.life.uiuc.edu/~gary/programs/fastDNAml.html
-
-fastDNAml is an attempt to solve the same problem as Joseph Felsenstein's
-DNAML, but to do so faster and using less memory, so that larger trees and/or
-more bootstrap replicates become tractable. Much of fastDNAml is merely a
-recoding of the PHYLIP 3.3 DNAML program from PASCAL to C. 
-
-For Felsenstein's phylogenetic analysis softwares, including the latest
-versions of DNAML, visit the PHYLIP Home Page:
-	http://evolution.genetics.washington.edu/phylip.html
-
-When publishing work that based on results from fastDNAml please cite:
-
-   Felsenstein, J.  1981.  Evolutionary trees from DNA sequences:
-   A maximum likelihood approach.  J. Mol. Evol. 17: 368-376.
-
-   Olsen, G. J., Matsuda, H., Hagstrom, R., and Overbeek, R.  1994.
-   fastDNAml:  A tool for construction of phylogenetic trees of DNA
-   sequences using maximum likelihood.  Comput. Appl. Biosci. 10: 41-48.
+WWW: http://www.life.illinois.edu/gary/programs/fastDNAml.html
>Release-Note:
>Audit-Trail:
>Unformatted: