ports/68238: [new port] biology/blast
Fernan Aguero
fernan at iib.unsam.edu.ar
Wed Jun 23 12:50:35 UTC 2004
>Number: 68238
>Category: ports
>Synopsis: [new port] biology/blast
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: maintainer-update
>Submitter-Id: current-users
>Arrival-Date: Wed Jun 23 12:50:22 GMT 2004
>Closed-Date:
>Last-Modified:
>Originator: Fernan Aguero
>Release: FreeBSD 4.10-RELEASE i386
>Organization:
IIB-UNSAM
>Environment:
FreeBSD pi.iib.unsam.edu.ar 4.10-RELEASE FreeBSD 4.10-RELEASE #0: Wed May 26 12:56:43 ART 2004 fernan at pi.iib.unsam.edu.ar:/usr/obj/usr/src/sys/PI i386
>Description:
This is a port of the Washington University BLAST
(blast.wustl.edu).
The software is distributed in binary form and should be
obtained after signing a license agreement, which is free for
academia.
The port has been thus marked as RESTRICTED because it is not
allowed to create nor distribute a binary package in any way,
neither mirroring the application's DISTFILES.
For /usr/ports/LEGAL "No redistribution allowed" should be fine.
I'm CCing the software author, which has been more than helpful
in providing binaries for both FreeBSD-4 and 5 upon request.
Thanks Warren!
>How-To-Repeat:
>Fix:
--- blast.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:
#
# blast
# blast/Makefile
# blast/distinfo
# blast/pkg-message
# blast/pkg-descr
# blast/pkg-plist
#
echo c - blast
mkdir -p blast > /dev/null 2>&1
echo x - blast/Makefile
sed 's/^X//' >blast/Makefile << 'END-of-blast/Makefile'
X# vim:ts=8:sw=8:number:nowrap
X# New ports collection makefile for: WU BLAST
X# Date created: 27 May 2004
X# Whom: Fernan Aguero <fernan at iib.unsam.edu.ar>
X#
X# $FreeBSD$
X#
X
XPORTNAME= blast
XPORTVERSION= 2
XCATEGORIES= biology
XMASTER_SITES= #
XEXTRACT_SUFX= .tar.Z
X
XMAINTAINER= fernan at iib.unsam.edu.ar
XCOMMENT= WU BLAST, a software package for sequence similarity searches
X
XRESTRICTED= "License does not allow redistribution of binaries. You should first register for the software, which is free for academic use."
XONLY_FOR_ARCHS= i386
X
XNO_BUILD= yes
XDOWNLOAD_URL= http://blast.wustl.edu/licensing
X
XNO_WRKSUBDIR= yes
XUSE_REINPLACE= yes
X
XDOCS= COPYRIGHT FAQ-Indexing.html HISTORY LICENSE Memory.html \
X README.html parameters.html
XBINS= blasta gb2fasta gt2fasta memfile nrdb pam patdb \
X pir2fasta sp2fasta xdformat xdget
XSCRIPTS= wu-blastall wu-formatdb
XBLASTA_LINKS= blastn blastp blastx tblastn tblastx
XXDFORMAT_LINKS= setdb pressdb
X
X.include <bsd.port.pre.mk>
X
X.if ${OSVERSION} < 500000
XDISTNAME= ${PORTNAME}${PORTVERSION}.freebsd-4.x-i686
X.else
XDISTNAME= ${PORTNAME}${PORTVERSION}.freebsd-i686
X.endif
X
X.if !exists(${DISTDIR}/${DISTNAME}${EXTRACT_SUFX})
XIGNORE= "You must manually fetch ${PORTNAME}${PORTVERSION} for the FreeBSD platform \(${DISTNAME}${EXTRACT_SUFX}\) from ${DOWNLOAD_URL}, place it in ${DISTDIR} and then run make again"
X.endif
X
Xdo-install:
X
X.for bin in ${BINS}
X ${INSTALL_PROGRAM} ${WRKSRC}/${bin} ${PREFIX}/bin/
X.endfor
X
X.for script in ${SCRIPTS}
X ${INSTALL_SCRIPT} ${WRKSRC}/${script} ${PREFIX}/bin/
X.endfor
X
X ${CHMOD} a-r ${PREFIX}/bin/blasta
X
X.for blink in ${BLASTA_LINKS}
X @(cd ${PREFIX}/bin && ${LN} -s blasta ${blink})
X.endfor
X
X.for xlink in ${XDFORMAT_LINKS}
X @(cd ${PREFIX}/bin && ${LN} -s xdformat ${xlink})
X.endfor
X
X.if !defined (NOPORTDOCS)
X @${MKDIR} ${DOCSDIR}
X
X.for doc in ${DOCS}
X ${INSTALL_MAN} ${WRKSRC}/${doc} ${DOCSDIR}
X.endfor
X
X.endif
X
X @${MKDIR} ${DATADIR}
X ${CP} -R ${WRKSRC}/matrix ${DATADIR}
X ${CP} -R ${WRKSRC}/filter ${DATADIR}
X ${CP} ${WRKSRC}/sysblast.sample ${DATADIR}
X
Xpost-install:
X @${CP} ${PKGMESSAGE} ${PKGMESSAGE}.tmp
X ${REINPLACE_CMD} -e 's,%%DATADIR%%,${DATADIR},g' ${PKGMESSAGE}.tmp
X @${CAT} ${PKGMESSAGE}.tmp
X @${RM} ${PKGMESSAGE}.tmp
X
X.include <bsd.port.post.mk>
END-of-blast/Makefile
echo x - blast/distinfo
sed 's/^X//' >blast/distinfo << 'END-of-blast/distinfo'
XMD5 (blast2.freebsd-4.x-i686.tar.Z) = caf8944cbe64996943b84b3b694c233b
XSIZE (blast2.freebsd-4.x-i686.tar.Z) = 1562572
XMD5 (blast2.freebsd-i686.tar.Z) = 1394faf2ef93d2ab13419d940e724681
XSIZE (blast2.freebsd-i686.tar.Z) = 1589940
END-of-blast/distinfo
echo x - blast/pkg-message
sed 's/^X//' >blast/pkg-message << 'END-of-blast/pkg-message'
X======================================================================
X
XA sample configuration file has been installed in %%DATADIR%% and named
Xsysblast.sample. Edit it to suit your needs, rename it to 'sysblast' and
Xplace it under /etc so that it can be recognized at runtime by the blast
Xexecutable.
X
XMatrix files and filter executables have been placed in
X%%DATADIR%%/matrix and %%DATADIR%%/filter, respectively.
XYou should set environment variables WUBLASTMAT and WUBLASTFILTER
X(pointing to the respective directories) so that the blast executable
Xcan find them.
X
X======================================================================
END-of-blast/pkg-message
echo x - blast/pkg-descr
sed 's/^X//' >blast/pkg-descr << 'END-of-blast/pkg-descr'
XWashington University BLAST (WU BLAST) version 2.0 is a powerful
Xsoftware package for gene and protein identification, using sensitive,
Xselective and rapid similarity searches of protein and nucleotide
Xsequence databases. WU BLAST 2.0 builds upon WU BLAST 1.4, which in turn
Xwas based on the public domain NCBI BLAST version 1.4. While NCBI BLAST
Xand WU BLAST 1.4 are in the public domain, WU BLAST 2.0 contains
Xsignificant new features and extended capabilities, the development of
Xwhich began in late 1994, at Washington University in Saint Louis. First
Xreleased in May 1996, or more than a year ahead of the NCBI, WU BLAST
X2.0 is the original gapped BLAST with statistics and is known for
Xsetting higher standards for sensitivity, speed, correctness and
Xaccuracy, scalability and reliability than competing programs and
Ximplementations. WU BLAST is neither a re-hashed nor "Mac-ified" version
Xof NCBI BLAST, although WU BLAST in many ways is easier to use. WU BLAST
Xessentially shares no code with NCBI BLAST, except for portions that
Xboth packages derived from ungapped NCBI BLAST 1.4.
X
XWWW: http://blast.wustl.edu
END-of-blast/pkg-descr
echo x - blast/pkg-plist
sed 's/^X//' >blast/pkg-plist << 'END-of-blast/pkg-plist'
Xbin/blasta
Xbin/gb2fasta
Xbin/gt2fasta
Xbin/memfile
Xbin/nrdb
Xbin/pam
Xbin/patdb
Xbin/pir2fasta
Xbin/sp2fasta
Xbin/xdformat
Xbin/xdget
Xbin/wu-blastall
Xbin/wu-formatdb
Xbin/blastn
Xbin/blastp
Xbin/blastx
Xbin/tblastn
Xbin/tblastx
Xbin/setdb
Xbin/pressdb
Xshare/doc/blast/COPYRIGHT
Xshare/doc/blast/FAQ-Indexing.html
Xshare/doc/blast/HISTORY
Xshare/doc/blast/LICENSE
Xshare/doc/blast/Memory.html
Xshare/doc/blast/README.html
Xshare/doc/blast/parameters.html
Xshare/blast/matrix/aa/nuc.4.4
Xshare/blast/matrix/aa/BLOSUM30
Xshare/blast/matrix/aa/BLOSUM35
Xshare/blast/matrix/aa/BLOSUM40
Xshare/blast/matrix/aa/BLOSUM45
Xshare/blast/matrix/aa/BLOSUM50
Xshare/blast/matrix/aa/BLOSUM55
Xshare/blast/matrix/aa/BLOSUM60
Xshare/blast/matrix/aa/BLOSUM62
Xshare/blast/matrix/aa/BLOSUM65
Xshare/blast/matrix/aa/BLOSUM70
Xshare/blast/matrix/aa/BLOSUM75
Xshare/blast/matrix/aa/BLOSUM80
Xshare/blast/matrix/aa/BLOSUM85
Xshare/blast/matrix/aa/BLOSUM90
Xshare/blast/matrix/aa/BLOSUMN
Xshare/blast/matrix/aa/blosum100
Xshare/blast/matrix/aa/blosum30
Xshare/blast/matrix/aa/blosum35
Xshare/blast/matrix/aa/blosum40
Xshare/blast/matrix/aa/blosum45
Xshare/blast/matrix/aa/blosum50
Xshare/blast/matrix/aa/blosum55
Xshare/blast/matrix/aa/blosum60
Xshare/blast/matrix/aa/blosumn
Xshare/blast/matrix/aa/blosum62
Xshare/blast/matrix/aa/blosum65
Xshare/blast/matrix/aa/blosum70
Xshare/blast/matrix/aa/blosum75
Xshare/blast/matrix/aa/blosum80
Xshare/blast/matrix/aa/blosum85
Xshare/blast/matrix/aa/DAYHOFF
Xshare/blast/matrix/aa/GONNET
Xshare/blast/matrix/aa/IDENTITY
Xshare/blast/matrix/aa/MATCH
Xshare/blast/matrix/aa/PAM10
Xshare/blast/matrix/aa/NUC.4.2
Xshare/blast/matrix/aa/NUC.4.4
Xshare/blast/matrix/aa/PAM100
Xshare/blast/matrix/aa/PAM110
Xshare/blast/matrix/aa/PAM120
Xshare/blast/matrix/aa/PAM130
Xshare/blast/matrix/aa/PAM120.cdi
Xshare/blast/matrix/aa/PAM140
Xshare/blast/matrix/aa/PAM150
Xshare/blast/matrix/aa/PAM160
Xshare/blast/matrix/aa/PAM170
Xshare/blast/matrix/aa/PAM160.cdi
Xshare/blast/matrix/aa/PAM180
Xshare/blast/matrix/aa/PAM190
Xshare/blast/matrix/aa/PAM20
Xshare/blast/matrix/aa/PAM200
Xshare/blast/matrix/aa/PAM200.cdi
Xshare/blast/matrix/aa/PAM210
Xshare/blast/matrix/aa/PAM220
Xshare/blast/matrix/aa/PAM230
Xshare/blast/matrix/aa/PAM240
Xshare/blast/matrix/aa/PAM250
Xshare/blast/matrix/aa/PAM250.cdi
Xshare/blast/matrix/aa/PAM260
Xshare/blast/matrix/aa/PAM270
Xshare/blast/matrix/aa/PAM280
Xshare/blast/matrix/aa/PAM290
Xshare/blast/matrix/aa/PAM30
Xshare/blast/matrix/aa/PAM300
Xshare/blast/matrix/aa/PAM310
Xshare/blast/matrix/aa/PAM320
Xshare/blast/matrix/aa/PAM330
Xshare/blast/matrix/aa/PAM340
Xshare/blast/matrix/aa/PAM350
Xshare/blast/matrix/aa/PAM360
Xshare/blast/matrix/aa/PAM370
Xshare/blast/matrix/aa/PAM380
Xshare/blast/matrix/aa/PAM390
Xshare/blast/matrix/aa/PAM40
Xshare/blast/matrix/aa/PAM40.cdi
Xshare/blast/matrix/aa/PAM400
Xshare/blast/matrix/aa/PAM410
Xshare/blast/matrix/aa/PAM420
Xshare/blast/matrix/aa/PAM430
Xshare/blast/matrix/aa/PAM440
Xshare/blast/matrix/aa/PAM450
Xshare/blast/matrix/aa/PAM460
Xshare/blast/matrix/aa/PAM470
Xshare/blast/matrix/aa/PAM480
Xshare/blast/matrix/aa/PAM490
Xshare/blast/matrix/aa/PAM50
Xshare/blast/matrix/aa/PAM500
Xshare/blast/matrix/aa/PAM60
Xshare/blast/matrix/aa/PAM70
Xshare/blast/matrix/aa/PAM80
Xshare/blast/matrix/aa/PAM80.cdi
Xshare/blast/matrix/aa/PAM90
Xshare/blast/matrix/aa/blosum90
Xshare/blast/matrix/aa/pam120.cdi
Xshare/blast/matrix/aa/pam160.cdi
Xshare/blast/matrix/aa/dayhoff
Xshare/blast/matrix/aa/gonnet
Xshare/blast/matrix/aa/identity
Xshare/blast/matrix/aa/match
Xshare/blast/matrix/aa/pam10
Xshare/blast/matrix/aa/pam100
Xshare/blast/matrix/aa/pam110
Xshare/blast/matrix/aa/pam120
Xshare/blast/matrix/aa/pam130
Xshare/blast/matrix/aa/pam140
Xshare/blast/matrix/aa/pam150
Xshare/blast/matrix/aa/pam160
Xshare/blast/matrix/aa/pam170
Xshare/blast/matrix/aa/pam180
Xshare/blast/matrix/aa/pam190
Xshare/blast/matrix/aa/pam20
Xshare/blast/matrix/aa/pam200
Xshare/blast/matrix/aa/pam250.cdi
Xshare/blast/matrix/aa/pam210
Xshare/blast/matrix/aa/pam220
Xshare/blast/matrix/aa/pam230
Xshare/blast/matrix/aa/pam240
Xshare/blast/matrix/aa/pam250
Xshare/blast/matrix/aa/pam40.cdi
Xshare/blast/matrix/aa/pam260
Xshare/blast/matrix/aa/pam270
Xshare/blast/matrix/aa/pam280
Xshare/blast/matrix/aa/pam290
Xshare/blast/matrix/aa/pam30
Xshare/blast/matrix/aa/pam300
Xshare/blast/matrix/aa/pam310
Xshare/blast/matrix/aa/pam320
Xshare/blast/matrix/aa/pam330
Xshare/blast/matrix/aa/pam340
Xshare/blast/matrix/aa/pam350
Xshare/blast/matrix/aa/pam360
Xshare/blast/matrix/aa/pam370
Xshare/blast/matrix/aa/pam380
Xshare/blast/matrix/aa/pam390
Xshare/blast/matrix/aa/pam40
Xshare/blast/matrix/aa/pam80.cdi
Xshare/blast/matrix/aa/pam400
Xshare/blast/matrix/aa/pam410
Xshare/blast/matrix/aa/pam420
Xshare/blast/matrix/aa/pam430
Xshare/blast/matrix/aa/pam440
Xshare/blast/matrix/aa/pam450
Xshare/blast/matrix/aa/pam460
Xshare/blast/matrix/aa/pam470
Xshare/blast/matrix/aa/pam480
Xshare/blast/matrix/aa/pam490
Xshare/blast/matrix/aa/pam50
Xshare/blast/matrix/aa/pam500
Xshare/blast/matrix/aa/pam60
Xshare/blast/matrix/aa/pam70
Xshare/blast/matrix/aa/pam80
Xshare/blast/matrix/aa/pam90
Xshare/blast/matrix/aa/pam200.cdi
Xshare/blast/matrix/aa/PHAT_T70_B66
Xshare/blast/matrix/aa/PHAT_T75_B73
Xshare/blast/matrix/aa/PHAT_T80_B78
Xshare/blast/matrix/aa/PHAT_T85_B82
Xshare/blast/matrix/aa/phat_t70_b66
Xshare/blast/matrix/aa/phat_t75_b73
Xshare/blast/matrix/aa/phat_t80_b78
Xshare/blast/matrix/aa/phat_t85_b82
Xshare/blast/matrix/aa/nuc.4.2
Xshare/blast/matrix/aa/BLOSUM100
Xshare/blast/matrix/nt/PUPY.4.4
Xshare/blast/matrix/nt/IDENTITY.4.2
Xshare/blast/matrix/nt/IDENTITY.4.4
Xshare/blast/matrix/nt/identity.4.2
Xshare/blast/matrix/nt/pupy.4.2
Xshare/blast/matrix/nt/pupy.4.4
Xshare/blast/matrix/nt/PUPY.4.2
Xshare/blast/matrix/nt/identity.4.4
Xshare/blast/matrix/README
Xshare/blast/filter/seg
Xshare/blast/filter/seg+xnu
Xshare/blast/filter/xnu+seg
Xshare/blast/filter/nseg
Xshare/blast/filter/dust
Xshare/blast/filter/nmerge
Xshare/blast/filter/xnu
Xshare/blast/filter/pmerge
Xshare/blast/filter/pseg
Xshare/blast/filter/README
Xshare/blast/sysblast.sample
X at dirrm share/doc/blast
X at dirrm share/blast/matrix/aa
X at dirrm share/blast/matrix/nt
X at dirrm share/blast/matrix
X at dirrm share/blast/filter
X at dirrm share/blast
END-of-blast/pkg-plist
exit
--- blast.shar ends here ---
>Release-Note:
>Audit-Trail:
>Unformatted:
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