Date: Thu, 31 Oct 2013 19:40:06 GMT From: KATO Tsuguru <tkato432@yahoo.com> To: freebsd-ports-bugs@FreeBSD.org Subject: Re: ports/172496: biology/blat: Update to version 35 Message-ID: <201310311940.r9VJe61X065452@freefall.freebsd.org>
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The following reply was made to PR ports/172496; it has been noted by GNATS. From: KATO Tsuguru <tkato432@yahoo.com> To: bug-followup@FreeBSD.org Cc: Subject: Re: ports/172496: biology/blat: Update to version 35 Date: Fri, 1 Nov 2013 04:25:33 +0900 This is a multi-part message in MIME format. --Multipart=_Fri__1_Nov_2013_04_25_33_+0900_fsq_ImQqfDQNdKuY Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Remake of the patch against current tree. --Multipart=_Fri__1_Nov_2013_04_25_33_+0900_fsq_ImQqfDQNdKuY Content-Type: text/x-diff; name="biology_blat.diff" Content-Disposition: attachment; filename="biology_blat.diff" Content-Transfer-Encoding: 7bit diff -urN /usr/ports/biology/blat/Makefile biology/blat/Makefile --- /usr/ports/biology/blat/Makefile 2013-09-22 01:13:54.000000000 +0900 +++ biology/blat/Makefile 2013-11-01 00:00:00.000000000 +0900 @@ -2,55 +2,68 @@ # $FreeBSD: head/biology/blat/Makefile 327709 2013-09-20 15:55:44Z 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/ DISTNAME= ${PORTNAME}Src${PORTVERSION} 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 + 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}" + +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 -PLIST_FILES+= ${EXECUTABLES:S,^,bin/,} -PORTDOCS= README -PORTDATA= * - -OPTIONS_DEFINE= DOCS +.include <bsd.port.options.mk> -NO_STAGE= yes post-patch: @${MKDIR} ${WRKSRC}/bin/${ARCH} @${MKDIR} ${WRKSRC}/lib/${ARCH} - @${REINPLACE_CMD} -E 's,^(CC|CFLAGS)=,\1 ?=,g;s,-Werror,,g' \ - ${WRKSRC}/inc/common.mk - -.include <bsd.port.options.mk> + @${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=|' ${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} \ + ${STAGEDIR}${PREFIX}/bin) .endfor - @${MKDIR} ${DATADIR}/webBlat - ${INSTALL_PROGRAM} ${WRKSRC}/webBlat/webBlat ${DATADIR}/webBlat - ${INSTALL_DATA} ${WRKSRC}/webBlat/install.txt ${DATADIR}/webBlat -.if ${PORT_OPTIONS:MDOCS} - @${MKDIR} ${DOCSDIR} - ${INSTALL_DATA} ${WRKSRC}/README ${DOCSDIR} -.endif - -post-install: - @${ECHO_MSG} - @${CAT} ${PKGMESSAGE} - @${ECHO_MSG} + @${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} + (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 2013-06-21 03:53:41.000000000 +0900 +++ biology/blat/distinfo 2013-11-01 00:00:00.000000000 +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/pkg-message.in biology/blat/files/pkg-message.in --- /usr/ports/biology/blat/files/pkg-message.in 2013-06-21 03:53:41.000000000 +0900 +++ biology/blat/files/pkg-message.in 2013-11-01 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 2013-06-21 03:53:41.000000000 +0900 +++ biology/blat/pkg-descr 2013-11-01 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/ --Multipart=_Fri__1_Nov_2013_04_25_33_+0900_fsq_ImQqfDQNdKuY--
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