Date: Wed, 23 Jun 2004 09:41:43 -0300 (ART) From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: FreeBSD-gnats-submit@FreeBSD.org Cc: Warren Gish <gish@watson.wustl.edu> Subject: ports/68238: [new port] biology/blast Message-ID: <200406231241.i5NCfhgg016075@pi.iib.unsam.edu.ar> Resent-Message-ID: <200406231250.i5NCoOH3034437@freefall.freebsd.org>
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>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@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@iib.unsam.edu.ar> X# X# $FreeBSD$ X# X XPORTNAME= blast XPORTVERSION= 2 XCATEGORIES= biology XMASTER_SITES= # XEXTRACT_SUFX= .tar.Z X XMAINTAINER= fernan@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@dirrm share/doc/blast X@dirrm share/blast/matrix/aa X@dirrm share/blast/matrix/nt X@dirrm share/blast/matrix X@dirrm share/blast/filter X@dirrm share/blast END-of-blast/pkg-plist exit --- blast.shar ends here --- >Release-Note: >Audit-Trail: >Unformatted:
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