Date: Thu, 27 Feb 2014 11:46:11 +0000 (UTC) From: Martin Wilke <miwi@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r346318 - in head/biology/blat: . files Message-ID: <201402271146.s1RBkBi7019373@svn.freebsd.org>
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Author: miwi Date: Thu Feb 27 11:46:11 2014 New Revision: 346318 URL: http://svnweb.freebsd.org/changeset/ports/346318 QAT: https://qat.redports.org/buildarchive/r346318/ Log: - Update to 35 PR: 184245 Modified: head/biology/blat/Makefile head/biology/blat/distinfo head/biology/blat/files/pkg-message.in head/biology/blat/pkg-descr Modified: head/biology/blat/Makefile ============================================================================== --- head/biology/blat/Makefile Thu Feb 27 11:45:26 2014 (r346317) +++ head/biology/blat/Makefile Thu Feb 27 11:46:11 2014 (r346318) @@ -2,45 +2,68 @@ # $FreeBSD$ 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@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> Modified: head/biology/blat/distinfo ============================================================================== --- head/biology/blat/distinfo Thu Feb 27 11:45:26 2014 (r346317) +++ head/biology/blat/distinfo Thu Feb 27 11:46:11 2014 (r346318) @@ -1,2 +1,2 @@ -SHA256 (blatSrc34.zip) = b764828fdf8ef4c9994ae4b6148340a776493475edb573b6adf63ae7ca9b2629 -SIZE (blatSrc34.zip) = 2142975 +SHA256 (blatSrc35.zip) = 06d9bcf114ec4a4b21fef0540a0532556b6602322a5a2b33f159dc939ae53620 +SIZE (blatSrc35.zip) = 1886214 Modified: head/biology/blat/files/pkg-message.in ============================================================================== --- head/biology/blat/files/pkg-message.in Thu Feb 27 11:45:26 2014 (r346317) +++ head/biology/blat/files/pkg-message.in Thu Feb 27 11:46:11 2014 (r346318) @@ -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 =============================================================================== Modified: head/biology/blat/pkg-descr ============================================================================== --- head/biology/blat/pkg-descr Thu Feb 27 11:45:26 2014 (r346317) +++ head/biology/blat/pkg-descr Thu Feb 27 11:46:11 2014 (r346318) @@ -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 @@ genome (but not the genome itself) in me 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/
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