ports/93060: [ new port ] Jim Kent's BLAT

[Fernan Aguero]

>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 at 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 at 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 at 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 at dirrm %%DATADIR%%/webBlat
X at 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: