ports/184245: biology/blat: Update to version 35

Sun Nov 24 18:10:09 UTC 2013

>Number:         184245
>Category:       ports
>Synopsis:       biology/blat: Update to version 35
>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:   Sun Nov 24 18:10:08 UTC 2013
>Closed-Date:
>Last-Modified:
>Originator:     KATO Tsuguru
>Release:        FreeBSD 8.4-RELEASE-p4 i386
>Organization:
>Environment:
>Description:
- Update to version 35

>How-To-Repeat:
>Fix:

diff -urN /usr/ports/biology/blat/Makefile biology/blat/Makefile

--- /usr/ports/biology/blat/Makefile	2013-11-13 17:50:18.000000000 +0900
+++ biology/blat/Makefile	2013-11-25 00:00:00.000000000 +0900
@@ -2,45 +2,68 @@
 # $FreeBSD: head/biology/blat/Makefile 333628 2013-11-12 22:02:02Z bapt $
 
 PORTNAME=	blat
-PORTVERSION=	34
+PORTVERSION=	35
 CATEGORIES=	biology
-MASTER_SITES=	http://www.soe.ucsc.edu/~kent/src/
+MASTER_SITES=	http://hgwdev.cse.ucsc.edu/~kent/src/ \
+		http://users.soe.ucsc.edu/~kent/src/
 DISTNAME=	${PORTNAME}Src${PORTVERSION}
+EXTRACT_SUFX=	.zip
 
 MAINTAINER=	ports at FreeBSD.org
 COMMENT=	Fast tool for local sequence similarity searches
 
+LIB_DEPENDS=	libpng15.so:${PORTSDIR}/graphics/png
+
+OPTIONS_DEFINE=	DOCS
+
+WRKSRC=		${WRKDIR}/${PORTNAME}Src
+
 USES=		gmake
-EXTRACT_SUFX=	.zip
+USE_OPENSSL=	yes
 MAKEFILE=	makefile
-WRKSRC=		${WRKDIR}/${PORTNAME}Src
-MAKE_ENV+=	HOME="${WRKSRC}/${BINDIR}" MACHTYPE="${ARCH}"
+MAKE_ENV=	MACHTYPE="${ARCH}" HOME="${WRKSRC}/${BINDIR}" STRIP="${TRUE}"
+
+CPPFLAGS+=	$$(libpng-config --cflags)
+LDFLAGS+=	$$(libpng-config --ldflags)
 
 SUB_FILES=	pkg-message
 
+PORTDOCS=	README
+PLIST_FILES=	${EXECUTABLES:S,^,bin/,} \
+		lib/blat/webBlat/webBlat \
+		lib/blat/webBlat/install.txt
+PLIST_DIRS=	lib/blat/webBlat \
+		lib/blat
+
 EXECUTABLES=	blat faToNib faToTwoBit gfClient gfServer nibFrag \
 		pslPretty pslReps pslSort twoBitInfo twoBitToFa
 
-PLIST_FILES+=	${EXECUTABLES:S,^,bin/,}
-PORTDOCS=	README
-PORTDATA=	*
-
-OPTIONS_DEFINE=	DOCS
+.include <bsd.port.options.mk>
 
 post-patch:
 	@${MKDIR} ${WRKSRC}/bin/${ARCH}
 	@${MKDIR} ${WRKSRC}/lib/${ARCH}
-	@${REINPLACE_CMD} -E 's,^(CC|CFLAGS)=,\1 ?=,g;s,-Werror,,g' \
-		${WRKSRC}/inc/common.mk
+	@${FIND} ${WRKSRC} -name "makefile" | ${XARGS} ${REINPLACE_CMD} -e \
+		's|$${DESTDIR}||g'
+	@${REINPLACE_CMD} -e \
+		's|cd |$$(MAKE) -C | ; \
+		 s| &&.*||' ${WRKSRC}/makefile
+	@${REINPLACE_CMD} -e \
+		's|^CC=|CC?=| ; \
+		 s|^COPT=.*|COPT=$${CPPFLAGS}| ; \
+		 s|^L=.*|L=$${LDFLAGS}|' ${WRKSRC}/inc/common.mk
 
 do-install:
 .for exe in ${EXECUTABLES}
-	${INSTALL_PROGRAM} ${WRKSRC}/bin/${ARCH}/${exe} ${STAGEDIR}${PREFIX}/bin
+	(cd ${WRKSRC}/bin/${ARCH} && ${INSTALL_PROGRAM} ${exe} \
+		${STAGEDIR}${PREFIX}/bin)
 .endfor
-	@${MKDIR} ${STAGEDIR}${DATADIR}/webBlat
-	${INSTALL_PROGRAM} ${WRKSRC}/webBlat/webBlat ${STAGEDIR}${DATADIR}/webBlat
-	${INSTALL_DATA} ${WRKSRC}/webBlat/install.txt ${STAGEDIR}${DATADIR}/webBlat
+	@${MKDIR} ${STAGEDIR}${PREFIX}/lib/blat/webBlat
+	(cd ${WRKSRC}/webBlat && ${INSTALL_PROGRAM} webBlat \
+		${STAGEDIR}${PREFIX}/lib/blat/webBlat)
+	(cd ${WRKSRC}/webBlat && ${INSTALL_DATA} install.txt \
+		${STAGEDIR}${PREFIX}/lib/blat/webBlat)
 	@${MKDIR} ${STAGEDIR}${DOCSDIR}
-	${INSTALL_DATA} ${WRKSRC}/README ${STAGEDIR}${DOCSDIR}
+	(cd ${WRKSRC} && ${INSTALL_DATA} README ${STAGEDIR}${DOCSDIR})
 
 .include <bsd.port.mk>
diff -urN /usr/ports/biology/blat/distinfo biology/blat/distinfo
--- /usr/ports/biology/blat/distinfo	2013-11-06 22:05:44.000000000 +0900
+++ biology/blat/distinfo	2013-11-25 00:00:00.000000000 +0900
@@ -1,2 +1,2 @@
-SHA256 (blatSrc34.zip) = b764828fdf8ef4c9994ae4b6148340a776493475edb573b6adf63ae7ca9b2629
-SIZE (blatSrc34.zip) = 2142975
+SHA256 (blatSrc35.zip) = 06d9bcf114ec4a4b21fef0540a0532556b6602322a5a2b33f159dc939ae53620
+SIZE (blatSrc35.zip) = 1886214
diff -urN /usr/ports/biology/blat/files/pkg-message.in biology/blat/files/pkg-message.in
--- /usr/ports/biology/blat/files/pkg-message.in	2013-11-06 22:05:44.000000000 +0900
+++ biology/blat/files/pkg-message.in	2013-11-25 00:00:00.000000000 +0900
@@ -3,6 +3,6 @@
  A CGI script (webBlat) and instructions on how to set up a BLAT web server
  have been installed in 
  
- %%DATADIR%%
+ %%PREFIX%%/lib/blat
 
 ===============================================================================
diff -urN /usr/ports/biology/blat/pkg-descr biology/blat/pkg-descr
--- /usr/ports/biology/blat/pkg-descr	2013-11-06 22:05:44.000000000 +0900
+++ biology/blat/pkg-descr	2013-11-25 00:00:00.000000000 +0900
@@ -1,9 +1,9 @@
-BLAT is a bioinformatics software tool which performs rapid mRNA/DNA
-and cross-species protein alignments. BLAT is more accurate and 500
-times faster than popular existing tools for mRNA/DNA alignments and 50
-times faster for protein alignments at sensitivity settings typically
-used when comparing vertebrate sequences. (Source: Kent, W.J. 2002. BLAT
--- The BLAST-Like Alignment Tool. Genome Research 4: 656-664.
+BLAT is a bioinformatics software tool which performs rapid mRNA/DNA and
+cross-species protein alignments. BLAT is more accurate and 500 times
+faster than popular existing tools for mRNA/DNA alignments and 50 times
+faster for protein alignments at sensitivity settings typically used
+when comparing vertebrate sequences. (Source: Kent, W.J. 2002. BLAT --
+The BLAST-Like Alignment Tool. Genome Research 4: 656-664.
 http://dx.doi.org/10.1101/gr.229202)
 
 BLAT is not BLAST. DNA BLAT works by keeping an index of the entire
@@ -11,4 +11,4 @@
 bit less than a gigabyte of RAM, BLAT can deliver high performance on a
 reasonably priced Linux box.
 
-WWW: http://www.genomeblat.com
+WWW: http://users.soe.ucsc.edu/~kent/
>Release-Note:
>Audit-Trail:
>Unformatted:
