Date: Wed, 8 Feb 2006 16:22:46 -0300 (ART) From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/93060: [ new port ] Jim Kent's BLAT Message-ID: <200602081922.k18JMkrZ043189@omega.iib.unsam.edu.ar> Resent-Message-ID: <200602081930.k18JUDmM010818@freefall.freebsd.org>
next in thread | raw e-mail | index | archive | help
>Number: 93060 >Category: ports >Synopsis: [ new port ] Jim Kent's BLAT >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: Wed Feb 08 19:30:12 GMT 2006 >Closed-Date: >Last-Modified: >Originator: Fernan Aguero >Release: FreeBSD 6.0-RELEASE-p4 i386 >Organization: IIB-UNSAM >Environment: System: FreeBSD omega.iib.unsam.edu.ar 6.0-RELEASE-p4 FreeBSD 6.0-RELEASE-p4 #0: Wed Jan 25 12:43:39 ART 2006 fernan@omega.iib.unsam.edu.ar:/usr/obj/usr/src/sys/OMEGA i386 >Description: >How-To-Repeat: >Fix: --- blat.shar begins here --- # This is a shell archive. Save it in a file, remove anything before # this line, and then unpack it by entering "sh file". Note, it may # create directories; files and directories will be owned by you and # have default permissions. # # This archive contains: # # blat # blat/Makefile # blat/pkg-descr # blat/distinfo # blat/pkg-plist # blat/files # blat/files/pkg-message.in # echo c - blat mkdir -p blat > /dev/null 2>&1 echo x - blat/Makefile sed 's/^X//' >blat/Makefile << 'END-of-blat/Makefile' X# ex:ts=8 X# New ports collection makefile for: blat X# Date created: 08 Dec 2005 X# Whom: Fernan Aguero <fernan@iib.unsam.edu.ar> X# X# $FreeBSD$ X# X XPORTNAME= blat XPORTVERSION= 33 XCATEGORIES= biology XMASTER_SITES= http://www.soe.ucsc.edu/~kent/src/ XDISTNAME= ${PORTNAME}Src${PORTVERSION} X XMAINTAINER= fernan@iib.unsam.edu.ar XCOMMENT= A fast tool for local sequence similarity searches X XUSE_ZIP= yes XUSE_GMAKE= yes XUSE_GCC= 3.4+ XMAKEFILE= makefile XWRKSRC= ${WRKDIR}/${PORTNAME}Src XMAKE_ENV+= HOME="${WRKSRC}/${BINDIR}" X XSUB_FILES= pkg-message X XEXECUTABLES= blat faToNib faToTwoBit gfClient gfServer nibFrag \ X pslPretty pslReps pslSort twoBitInfo twoBitToFa X Xpost-patch: X @${MKDIR} ${WRKSRC}/bin/${MACHTYPE} X @${MKDIR} ${WRKSRC}/lib/${MACHTYPE} X Xdo-install: X.for exe in ${EXECUTABLES} X ${INSTALL_PROGRAM} ${WRKSRC}/bin/${MACHTYPE}/${exe} ${PREFIX}/bin X.endfor X ${MKDIR} ${DATADIR}/webBlat X ${INSTALL_PROGRAM} ${WRKSRC}/webBlat/webBlat ${DATADIR}/webBlat X ${INSTALL_DATA} ${WRKSRC}/webBlat/install.txt ${DATADIR}/webBlat X.if !defined(NOPORTDOCS) X ${MKDIR} ${DOCSDIR} X ${INSTALL_DATA} ${WRKSRC}/README ${DOCSDIR} X.endif X Xpost-install: X @${CAT} ${PKGMESSAGE} X X.include <bsd.port.mk> END-of-blat/Makefile echo x - blat/pkg-descr sed 's/^X//' >blat/pkg-descr << 'END-of-blat/pkg-descr' XBLAT is a bioinformatics software tool which performs rapid mRNA/DNA Xand cross-species protein alignments. BLAT is more accurate and 500 Xtimes faster than popular existing tools for mRNA/DNA alignments and 50 Xtimes faster for protein alignments at sensitivity settings typically Xused when comparing vertebrate sequences. (Source: Kent, W.J. 2002. BLAT X-- The BLAST-Like Alignment Tool. Genome Research 4: 656-664. Xhttp://dx.doi.org/10.1101/gr.229202) X XBLAT is not BLAST. DNA BLAT works by keeping an index of the entire Xgenome (but not the genome itself) in memory. Since the index takes up a Xbit less than a gigabyte of RAM, BLAT can deliver high performance on a Xreasonably priced Linux box. X XWWW: http://www.genomeblat.com END-of-blat/pkg-descr echo x - blat/distinfo sed 's/^X//' >blat/distinfo << 'END-of-blat/distinfo' XMD5 (blatSrc33.zip) = 5f9d3a4a88e57dfc435b5dd465209918 XSHA256 (blatSrc33.zip) = 4ca932721f529d815e64b51940c94d8136faec52c6b8bf8c3fcd3706337d9a29 XSIZE (blatSrc33.zip) = 1308517 END-of-blat/distinfo echo x - blat/pkg-plist sed 's/^X//' >blat/pkg-plist << 'END-of-blat/pkg-plist' Xbin/blat Xbin/faToNib Xbin/faToTwoBit Xbin/gfClient Xbin/gfServer Xbin/nibFrag Xbin/pslPretty Xbin/pslReps Xbin/pslSort Xbin/twoBitInfo Xbin/twoBitToFa X%%PORTDOCS%%%%DOCSDIR%%/README X%%DATADIR%%/webBlat/webBlat X%%DATADIR%%/webBlat/install.txt X%%PORTDOCS%%@dirrm %%DOCSDIR%% X@dirrm %%DATADIR%%/webBlat X@dirrm %%DATADIR%% END-of-blat/pkg-plist echo c - blat/files mkdir -p blat/files > /dev/null 2>&1 echo x - blat/files/pkg-message.in sed 's/^X//' >blat/files/pkg-message.in << 'END-of-blat/files/pkg-message.in' X=============================================================================== X X A CGI script (webBlat) and instructions on how to set up a BLAT web server X have been installed in X X %%DATADIR%% X X=============================================================================== END-of-blat/files/pkg-message.in exit --- blat.shar ends here --- >Release-Note: >Audit-Trail: >Unformatted:
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?200602081922.k18JMkrZ043189>