Date: Tue, 9 Oct 2012 02:55:49 +0900 From: KATO Tsuguru <tkato432@yahoo.com> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/172496: biology/blat: Update to version 35 Message-ID: <20121009025549.29ff8f044ce7b1a0f6910dd6@yahoo.com> Resent-Message-ID: <201210081800.q98I0Ror085258@freefall.freebsd.org>
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>Number: 172496 >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: Mon Oct 08 18:00:27 UTC 2012 >Closed-Date: >Last-Modified: >Originator: KATO Tsuguru >Release: FreeBSD 7.4-RELEASE-p10 i386 >Organization: >Environment: >Description: - Update to version 35 New file: files/patch-makefile Remove file: pkg-plist >How-To-Repeat: >Fix: diff -urN /usr/ports/biology/blat/Makefile biology/blat/Makefile --- /usr/ports/biology/blat/Makefile 2012-10-01 23:45:16.000000000 +0900 +++ biology/blat/Makefile 2012-10-03 06:08:01.000000000 +0900 @@ -2,44 +2,65 @@ # $FreeBSD: ports/biology/blat/Makefile,v 1.8 2012/10/01 14:45:16 tabthorpe Exp $ 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/ DISTNAME= ${PORTNAME}Src${PORTVERSION} MAINTAINER= ports@FreeBSD.org COMMENT= A fast tool for local sequence similarity searches +LIB_DEPENDS= png15:${PORTSDIR}/graphics/png + +OPTIONS_DEFINE= DOCS + +WRKSRC= ${WRKDIR}/${PORTNAME}Src + USE_ZIP= yes +USE_OPENSSL= yes USE_GMAKE= yes MAKEFILE= makefile -WRKSRC= ${WRKDIR}/${PORTNAME}Src -MAKE_ENV+= HOME="${WRKSRC}/${BINDIR}" MACHTYPE="${ARCH}" +MAKE_ENV= MACHTYPE="${ARCH}" SSLDIR="${OPENSSLBASE}/include/openssl" \ + PNGLIB="${LDFLAGS}" PNGINCL="${CPPFLAGS}" \ + HOME="${WRKSRC}/${BINDIR}" STRIP="${TRUE}" +MAKE_JOBS_SAFE=yes + +CPPFLAGS+= $$(libpng-config --I_opts) +LDFLAGS+= $$(libpng-config --ldflags) SUB_FILES= pkg-message +PORTDOCS= README +PLIST_FILES= ${EXECUTABLES:S,^,bin/,} \ + lib/blat/webBlat/webBlat \ + lib/blat/webBlat/install.txt +PLIST_DIRS= lib/blat/webBlat \ + lib/blat + EXECUTABLES= blat faToNib faToTwoBit gfClient gfServer nibFrag \ pslPretty pslReps pslSort twoBitInfo twoBitToFa +.include <bsd.port.options.mk> + post-patch: @${MKDIR} ${WRKSRC}/bin/${ARCH} @${MKDIR} ${WRKSRC}/lib/${ARCH} - @${REINPLACE_CMD} -E 's,^(CC|CFLAGS)=,\1 ?=,g;s,-Werror,,g' \ - ${WRKSRC}/inc/common.mk + @${REINPLACE_CMD} -e \ + 's|^CC=|CC?=| ; \ + s|COPT=.*|COPT=|' ${WRKSRC}/inc/common.mk do-install: .for exe in ${EXECUTABLES} - ${INSTALL_PROGRAM} ${WRKSRC}/bin/${ARCH}/${exe} ${PREFIX}/bin + (cd ${WRKSRC}/bin/${ARCH} && ${INSTALL_PROGRAM} ${exe} ${PREFIX}/bin) .endfor - ${MKDIR} ${DATADIR}/webBlat - ${INSTALL_PROGRAM} ${WRKSRC}/webBlat/webBlat ${DATADIR}/webBlat - ${INSTALL_DATA} ${WRKSRC}/webBlat/install.txt ${DATADIR}/webBlat -.if !defined(NOPORTDOCS) - ${MKDIR} ${DOCSDIR} - ${INSTALL_DATA} ${WRKSRC}/README ${DOCSDIR} + @${MKDIR} ${PREFIX}/lib/blat/webBlat + (cd ${WRKSRC}/webBlat \ + && ${INSTALL_PROGRAM} webBlat ${PREFIX}/lib/blat/webBlat \ + && ${INSTALL_DATA} install.txt ${PREFIX}/lib/blat/webBlat) +.if ${PORT_OPTIONS:MDOCS} + @${MKDIR} ${DOCSDIR} + (cd ${WRKSRC} && ${INSTALL_DATA} README ${DOCSDIR}) .endif - -post-install: @${CAT} ${PKGMESSAGE} .include <bsd.port.mk> diff -urN /usr/ports/biology/blat/distinfo biology/blat/distinfo --- /usr/ports/biology/blat/distinfo 2011-03-19 21:29:29.000000000 +0900 +++ biology/blat/distinfo 2012-10-03 04:51:43.000000000 +0900 @@ -1,2 +1,2 @@ -SHA256 (blatSrc34.zip) = b764828fdf8ef4c9994ae4b6148340a776493475edb573b6adf63ae7ca9b2629 -SIZE (blatSrc34.zip) = 2142975 +SHA256 (blatSrc35.zip) = 2fb53c9489f9bd95f4119a526e6911f107a759eeb228ccc53b3bebb3aa6e50ab +SIZE (blatSrc35.zip) = 1887567 diff -urN /usr/ports/biology/blat/files/patch-makefile biology/blat/files/patch-makefile --- /usr/ports/biology/blat/files/patch-makefile 1970-01-01 09:00:00.000000000 +0900 +++ biology/blat/files/patch-makefile 2012-10-03 05:45:18.000000000 +0900 @@ -0,0 +1,36 @@ +--- makefile.orig 2012-08-14 09:15:05.000000000 +0900 ++++ makefile 2012-10-03 05:40:34.000000000 +0900 +@@ -1,18 +1,19 @@ + all: +- cd lib && ${MAKE} +- cd jkOwnLib && ${MAKE} +- cd blat && $(MAKE) +- cd gfClient && $(MAKE) +- cd gfServer && $(MAKE) +- cd hg/pslPretty && $(MAKE) +- cd hg/pslReps && $(MAKE) +- cd hg/pslSort && $(MAKE) +- cd utils/nibFrag && $(MAKE) +- cd utils/faToNib && $(MAKE) +- cd utils/faToTwoBit && $(MAKE) +- cd utils/twoBitToFa && $(MAKE) +- cd utils/twoBitInfo && $(MAKE) +- cd webBlat && $(MAKE) ++ ++ $(MAKE) -C lib ++ $(MAKE) -C jkOwnLib ++ $(MAKE) -C blat ++ $(MAKE) -C gfClient ++ $(MAKE) -C gfServer ++ $(MAKE) -C hg/pslPretty ++ $(MAKE) -C hg/pslReps ++ $(MAKE) -C hg/pslSort ++ $(MAKE) -C utils/nibFrag ++ $(MAKE) -C utils/faToNib ++ $(MAKE) -C utils/faToTwoBit ++ $(MAKE) -C utils/twoBitToFa ++ $(MAKE) -C utils/twoBitInfo ++ $(MAKE) -C webBlat + + clean: + rm -f */*.o */*/*.o lib/*/*.a diff -urN /usr/ports/biology/blat/files/pkg-message.in biology/blat/files/pkg-message.in --- /usr/ports/biology/blat/files/pkg-message.in 2006-03-15 19:26:12.000000000 +0900 +++ biology/blat/files/pkg-message.in 2012-10-03 04:55:04.000000000 +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 2006-03-15 19:26:11.000000000 +0900 +++ biology/blat/pkg-descr 2012-10-03 06:06:19.000000000 +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/ diff -urN /usr/ports/biology/blat/pkg-plist biology/blat/pkg-plist --- /usr/ports/biology/blat/pkg-plist 2006-03-15 19:26:11.000000000 +0900 +++ biology/blat/pkg-plist 1970-01-01 09:00:00.000000000 +0900 @@ -1,17 +0,0 @@ -bin/blat -bin/faToNib -bin/faToTwoBit -bin/gfClient -bin/gfServer -bin/nibFrag -bin/pslPretty -bin/pslReps -bin/pslSort -bin/twoBitInfo -bin/twoBitToFa -%%PORTDOCS%%%%DOCSDIR%%/README -%%DATADIR%%/webBlat/webBlat -%%DATADIR%%/webBlat/install.txt -%%PORTDOCS%%@dirrm %%DOCSDIR%% -@dirrm %%DATADIR%%/webBlat -@dirrm %%DATADIR%% >Release-Note: >Audit-Trail: >Unformatted:
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