Date: Tue, 27 Jul 2004 12:24:41 -0300 From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: Volker Stolz <vs@freebsd.org> Cc: FreeBSD GNATS PR Submission <freebsd-gnats-submit@freebsd.org> Subject: Re: ports/69636: [new port] biology/blast Message-ID: <20040727152441.GF31845@iib.unsam.edu.ar> In-Reply-To: <200407271302.i6RD2ojo065308@freefall.freebsd.org> References: <200407271302.i6RD2ojo065308@freefall.freebsd.org>
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--UoPmpPX/dBe4BELn Content-Type: text/plain; charset=us-ascii Content-Disposition: inline +----[ Volker Stolz <vs@freebsd.org> (27.Jul.2004 10:05): | | Synopsis: [new port] biology/blast | | State-Changed-From-To: open->feedback | State-Changed-By: vs | State-Changed-When: Tue Jul 27 13:02:25 GMT 2004 | State-Changed-Why: | Suggest improvements. | | http://www.freebsd.org/cgi/query-pr.cgi?pr=69636 | +----] Here is the port, corrected. Thanks for the suggestions! Fernan -- Fernan Aguero - fernan at iib.unsam.edu.ar Phone: +54 11 4580-7255/7 ext 310, Fax: +54 11 4752-9639 Check http://genoma.unsam.edu.ar/~fernan for more info. --UoPmpPX/dBe4BELn Content-Type: text/plain; charset=us-ascii Content-Disposition: attachment; filename="blast.shar" # 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= wu-blast XPORTVERSION= 2.0 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 XPKGMESSAGE= ${WRKDIR}/pkg-message 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 ${OSVERSION} < 500000 XDISTNAME= blast${PORTVERSION:S/.0//}.freebsd-4.x-i686 X.else XDISTNAME= blast${PORTVERSION:S/.0//}.freebsd-i686 X.endif X X.if !exists(${DISTDIR}/${DISTNAME}${EXTRACT_SUFX}) XIGNORE= "You must manually fetch ${PORTNAME}${PORTVERSION:S/.0//} 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-rw,a+x ${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 ${DATADIR} X Xpost-install: X @${SED} -e 's,%%DATADIR%%,${DATADIR},g' \ X < ${.CURDIR}/pkg-message > ${PKGMESSAGE} X @${CAT} ${PKGMESSAGE} 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) = 3426153dc9fda4bddc0aff5b86c95a11 XMD5 (blast2.freebsd-i686.tar.Z) = 399e1fa6e275152e0a764252909aa5b8 XSIZE (blast2.freebsd-4.x-i686.tar.Z) = 1555542 XSIZE (blast2.freebsd-i686.tar.Z) = 1590385 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====================================================================== 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 X%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT X%%PORTDOCS%%%%DOCSDIR%%/FAQ-Indexing.html X%%PORTDOCS%%%%DOCSDIR%%/HISTORY X%%PORTDOCS%%%%DOCSDIR%%/LICENSE X%%PORTDOCS%%%%DOCSDIR%%/Memory.html X%%PORTDOCS%%%%DOCSDIR%%/README.html X%%PORTDOCS%%%%DOCSDIR%%/parameters.html X%%DATADIR%%/matrix/aa/nuc.4.4 X%%DATADIR%%/matrix/aa/BLOSUM30 X%%DATADIR%%/matrix/aa/BLOSUM35 X%%DATADIR%%/matrix/aa/BLOSUM40 X%%DATADIR%%/matrix/aa/BLOSUM45 X%%DATADIR%%/matrix/aa/BLOSUM50 X%%DATADIR%%/matrix/aa/BLOSUM55 X%%DATADIR%%/matrix/aa/BLOSUM60 X%%DATADIR%%/matrix/aa/BLOSUM62 X%%DATADIR%%/matrix/aa/BLOSUM65 X%%DATADIR%%/matrix/aa/BLOSUM70 X%%DATADIR%%/matrix/aa/BLOSUM75 X%%DATADIR%%/matrix/aa/BLOSUM80 X%%DATADIR%%/matrix/aa/BLOSUM85 X%%DATADIR%%/matrix/aa/BLOSUM90 X%%DATADIR%%/matrix/aa/BLOSUMN X%%DATADIR%%/matrix/aa/blosum100 X%%DATADIR%%/matrix/aa/blosum30 X%%DATADIR%%/matrix/aa/blosum35 X%%DATADIR%%/matrix/aa/blosum40 X%%DATADIR%%/matrix/aa/blosum45 X%%DATADIR%%/matrix/aa/blosum50 X%%DATADIR%%/matrix/aa/blosum55 X%%DATADIR%%/matrix/aa/blosum60 X%%DATADIR%%/matrix/aa/blosumn X%%DATADIR%%/matrix/aa/blosum62 X%%DATADIR%%/matrix/aa/blosum65 X%%DATADIR%%/matrix/aa/blosum70 X%%DATADIR%%/matrix/aa/blosum75 X%%DATADIR%%/matrix/aa/blosum80 X%%DATADIR%%/matrix/aa/blosum85 X%%DATADIR%%/matrix/aa/DAYHOFF X%%DATADIR%%/matrix/aa/GONNET X%%DATADIR%%/matrix/aa/IDENTITY X%%DATADIR%%/matrix/aa/MATCH X%%DATADIR%%/matrix/aa/PAM10 X%%DATADIR%%/matrix/aa/NUC.4.2 X%%DATADIR%%/matrix/aa/NUC.4.4 X%%DATADIR%%/matrix/aa/PAM100 X%%DATADIR%%/matrix/aa/PAM110 X%%DATADIR%%/matrix/aa/PAM120 X%%DATADIR%%/matrix/aa/PAM130 X%%DATADIR%%/matrix/aa/PAM120.cdi X%%DATADIR%%/matrix/aa/PAM140 X%%DATADIR%%/matrix/aa/PAM150 X%%DATADIR%%/matrix/aa/PAM160 X%%DATADIR%%/matrix/aa/PAM170 X%%DATADIR%%/matrix/aa/PAM160.cdi X%%DATADIR%%/matrix/aa/PAM180 X%%DATADIR%%/matrix/aa/PAM190 X%%DATADIR%%/matrix/aa/PAM20 X%%DATADIR%%/matrix/aa/PAM200 X%%DATADIR%%/matrix/aa/PAM200.cdi X%%DATADIR%%/matrix/aa/PAM210 X%%DATADIR%%/matrix/aa/PAM220 X%%DATADIR%%/matrix/aa/PAM230 X%%DATADIR%%/matrix/aa/PAM240 X%%DATADIR%%/matrix/aa/PAM250 X%%DATADIR%%/matrix/aa/PAM250.cdi X%%DATADIR%%/matrix/aa/PAM260 X%%DATADIR%%/matrix/aa/PAM270 X%%DATADIR%%/matrix/aa/PAM280 X%%DATADIR%%/matrix/aa/PAM290 X%%DATADIR%%/matrix/aa/PAM30 X%%DATADIR%%/matrix/aa/PAM300 X%%DATADIR%%/matrix/aa/PAM310 X%%DATADIR%%/matrix/aa/PAM320 X%%DATADIR%%/matrix/aa/PAM330 X%%DATADIR%%/matrix/aa/PAM340 X%%DATADIR%%/matrix/aa/PAM350 X%%DATADIR%%/matrix/aa/PAM360 X%%DATADIR%%/matrix/aa/PAM370 X%%DATADIR%%/matrix/aa/PAM380 X%%DATADIR%%/matrix/aa/PAM390 X%%DATADIR%%/matrix/aa/PAM40 X%%DATADIR%%/matrix/aa/PAM40.cdi X%%DATADIR%%/matrix/aa/PAM400 X%%DATADIR%%/matrix/aa/PAM410 X%%DATADIR%%/matrix/aa/PAM420 X%%DATADIR%%/matrix/aa/PAM430 X%%DATADIR%%/matrix/aa/PAM440 X%%DATADIR%%/matrix/aa/PAM450 X%%DATADIR%%/matrix/aa/PAM460 X%%DATADIR%%/matrix/aa/PAM470 X%%DATADIR%%/matrix/aa/PAM480 X%%DATADIR%%/matrix/aa/PAM490 X%%DATADIR%%/matrix/aa/PAM50 X%%DATADIR%%/matrix/aa/PAM500 X%%DATADIR%%/matrix/aa/PAM60 X%%DATADIR%%/matrix/aa/PAM70 X%%DATADIR%%/matrix/aa/PAM80 X%%DATADIR%%/matrix/aa/PAM80.cdi X%%DATADIR%%/matrix/aa/PAM90 X%%DATADIR%%/matrix/aa/blosum90 X%%DATADIR%%/matrix/aa/pam120.cdi X%%DATADIR%%/matrix/aa/pam160.cdi X%%DATADIR%%/matrix/aa/dayhoff X%%DATADIR%%/matrix/aa/gonnet X%%DATADIR%%/matrix/aa/identity X%%DATADIR%%/matrix/aa/match X%%DATADIR%%/matrix/aa/pam10 X%%DATADIR%%/matrix/aa/pam100 X%%DATADIR%%/matrix/aa/pam110 X%%DATADIR%%/matrix/aa/pam120 X%%DATADIR%%/matrix/aa/pam130 X%%DATADIR%%/matrix/aa/pam140 X%%DATADIR%%/matrix/aa/pam150 X%%DATADIR%%/matrix/aa/pam160 X%%DATADIR%%/matrix/aa/pam170 X%%DATADIR%%/matrix/aa/pam180 X%%DATADIR%%/matrix/aa/pam190 X%%DATADIR%%/matrix/aa/pam20 X%%DATADIR%%/matrix/aa/pam200 X%%DATADIR%%/matrix/aa/pam250.cdi X%%DATADIR%%/matrix/aa/pam210 X%%DATADIR%%/matrix/aa/pam220 X%%DATADIR%%/matrix/aa/pam230 X%%DATADIR%%/matrix/aa/pam240 X%%DATADIR%%/matrix/aa/pam250 X%%DATADIR%%/matrix/aa/pam40.cdi X%%DATADIR%%/matrix/aa/pam260 X%%DATADIR%%/matrix/aa/pam270 X%%DATADIR%%/matrix/aa/pam280 X%%DATADIR%%/matrix/aa/pam290 X%%DATADIR%%/matrix/aa/pam30 X%%DATADIR%%/matrix/aa/pam300 X%%DATADIR%%/matrix/aa/pam310 X%%DATADIR%%/matrix/aa/pam320 X%%DATADIR%%/matrix/aa/pam330 X%%DATADIR%%/matrix/aa/pam340 X%%DATADIR%%/matrix/aa/pam350 X%%DATADIR%%/matrix/aa/pam360 X%%DATADIR%%/matrix/aa/pam370 X%%DATADIR%%/matrix/aa/pam380 X%%DATADIR%%/matrix/aa/pam390 X%%DATADIR%%/matrix/aa/pam40 X%%DATADIR%%/matrix/aa/pam80.cdi X%%DATADIR%%/matrix/aa/pam400 X%%DATADIR%%/matrix/aa/pam410 X%%DATADIR%%/matrix/aa/pam420 X%%DATADIR%%/matrix/aa/pam430 X%%DATADIR%%/matrix/aa/pam440 X%%DATADIR%%/matrix/aa/pam450 X%%DATADIR%%/matrix/aa/pam460 X%%DATADIR%%/matrix/aa/pam470 X%%DATADIR%%/matrix/aa/pam480 X%%DATADIR%%/matrix/aa/pam490 X%%DATADIR%%/matrix/aa/pam50 X%%DATADIR%%/matrix/aa/pam500 X%%DATADIR%%/matrix/aa/pam60 X%%DATADIR%%/matrix/aa/pam70 X%%DATADIR%%/matrix/aa/pam80 X%%DATADIR%%/matrix/aa/pam90 X%%DATADIR%%/matrix/aa/pam200.cdi X%%DATADIR%%/matrix/aa/PHAT_T70_B66 X%%DATADIR%%/matrix/aa/PHAT_T75_B73 X%%DATADIR%%/matrix/aa/PHAT_T80_B78 X%%DATADIR%%/matrix/aa/PHAT_T85_B82 X%%DATADIR%%/matrix/aa/phat_t70_b66 X%%DATADIR%%/matrix/aa/phat_t75_b73 X%%DATADIR%%/matrix/aa/phat_t80_b78 X%%DATADIR%%/matrix/aa/phat_t85_b82 X%%DATADIR%%/matrix/aa/nuc.4.2 X%%DATADIR%%/matrix/aa/BLOSUM100 X%%DATADIR%%/matrix/nt/PUPY.4.4 X%%DATADIR%%/matrix/nt/IDENTITY.4.2 X%%DATADIR%%/matrix/nt/IDENTITY.4.4 X%%DATADIR%%/matrix/nt/identity.4.2 X%%DATADIR%%/matrix/nt/pupy.4.2 X%%DATADIR%%/matrix/nt/pupy.4.4 X%%DATADIR%%/matrix/nt/PUPY.4.2 X%%DATADIR%%/matrix/nt/identity.4.4 X%%DATADIR%%/matrix/README X%%DATADIR%%/filter/seg X%%DATADIR%%/filter/seg+xnu X%%DATADIR%%/filter/xnu+seg X%%DATADIR%%/filter/nseg X%%DATADIR%%/filter/dust X%%DATADIR%%/filter/nmerge X%%DATADIR%%/filter/xnu X%%DATADIR%%/filter/pmerge X%%DATADIR%%/filter/pseg X%%DATADIR%%/filter/README X%%DATADIR%%/sysblast.sample X%%PORTDOCS%%@dirrm %%DOCSDIR%% X@dirrm %%DATADIR%%/matrix/aa X@dirrm %%DATADIR%%/matrix/nt X@dirrm %%DATADIR%%/matrix X@dirrm %%DATADIR%%/filter X@dirrm %%DATADIR%% END-of-blast/pkg-plist exit --UoPmpPX/dBe4BELn--
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