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mirror of https://git.FreeBSD.org/ports.git synced 2024-12-25 04:43:33 +00:00

- Update to 35

PR:		184245
This commit is contained in:
Martin Wilke 2014-02-27 11:46:11 +00:00
parent 5332d904dd
commit 4e739fcd1a
Notes: svn2git 2021-03-31 03:12:20 +00:00
svn path=/head/; revision=346318
4 changed files with 51 additions and 28 deletions

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@ -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
USES= gmake
EXTRACT_SUFX= .zip
MAKEFILE= makefile
LIB_DEPENDS= libpng15.so:${PORTSDIR}/graphics/png
OPTIONS_DEFINE= DOCS
WRKSRC= ${WRKDIR}/${PORTNAME}Src
MAKE_ENV+= HOME="${WRKSRC}/${BINDIR}" MACHTYPE="${ARCH}"
USES= gmake
USE_OPENSSL= yes
MAKEFILE= makefile
MAKE_ENV= MACHTYPE="${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>

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@ -1,2 +1,2 @@
SHA256 (blatSrc34.zip) = b764828fdf8ef4c9994ae4b6148340a776493475edb573b6adf63ae7ca9b2629
SIZE (blatSrc34.zip) = 2142975
SHA256 (blatSrc35.zip) = 06d9bcf114ec4a4b21fef0540a0532556b6602322a5a2b33f159dc939ae53620
SIZE (blatSrc35.zip) = 1886214

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@ -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
===============================================================================

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@ -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 memory. Since the index takes up a
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/