Date: Tue, 27 Jul 2004 12:10:23 GMT From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: freebsd-ports-bugs@FreeBSD.org Subject: Re: ports/69636: [new port] biology/blast Message-ID: <200407271210.i6RCANhC052597@freefall.freebsd.org>
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The following reply was made to PR ports/69636; it has been noted by GNATS. From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: FreeBSD-gnats-submit@FreeBSD.org, freebsd-ports-bugs@FreeBSD.org Cc: Subject: Re: ports/69636: [new port] biology/blast Date: Tue, 27 Jul 2004 09:08:03 -0300 --0ntfKIWw70PvrIHh Content-Type: text/plain; charset=us-ascii Content-Disposition: inline +----[ <FreeBSD-gnats-submit@FreeBSD.org> (26.Jul.2004 19:58): | | Thank you very much for your problem report. | It has the internal identification `ports/69636'. | The individual assigned to look at your | report is: freebsd-ports-bugs. | | You can access the state of your problem report at any time | via this link: | | http://www.freebsd.org/cgi/query-pr.cgi?pr=69636 | | >Category: ports | >Responsible: freebsd-ports-bugs | >Synopsis: [new port] biology/blast | >Arrival-Date: Mon Jul 26 22:50:18 GMT 2004 | +----] Here's the patch. 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. --0ntfKIWw70PvrIHh Content-Type: application/x-shar Content-Disposition: attachment; filename="blast.shar" Content-Transfer-Encoding: quoted-printable # This is a shell archive. Save it in a file, remove anything before=0A# t= his line, and then unpack it by entering "sh file". Note, it may=0A# creat= e directories; files and directories will be owned by you and=0A# have defa= ult permissions.=0A#=0A# This archive contains:=0A#=0A# blast=0A# blast/Mak= efile=0A# blast/distinfo=0A# blast/pkg-message=0A# blast/pkg-descr=0A# blas= t/pkg-plist=0A#=0Aecho c - blast=0Amkdir -p blast > /dev/null 2>&1=0Aecho x= - blast/Makefile=0Ased 's/^X//' >blast/Makefile << 'END-of-blast/Makefile'= =0AX# vim:ts=3D8:sw=3D8:number:nowrap=0AX# New ports collection makefile fo= r: WU BLAST=0AX# Date created: 27 May 2004=0AX# Whom: Fernan Aguer= o <fernan@iib.unsam.edu.ar>=0AX#=0AX# $FreeBSD$=0AX#=0AX=0AXPORTNAME=3D bla= st=0AXPORTVERSION=3D 2.0=0AXCATEGORIES=3D biology=0AXMASTER_SITES=3D #=0AXE= XTRACT_SUFX=3D .tar.Z=0AX=0AXMAINTAINER=3D fernan@iib.unsam.edu.ar=0AXCOMME= NT=3D WU BLAST, a software package for sequence similarity searches=0AX=0AX= RESTRICTED=3D "License does not allow redistribution of binaries. You shoul= d first register for the software, which is free for academic use."=0AXONLY= _FOR_ARCHS=3D i386=0AX=0AXNO_BUILD=3D yes=0AXDOWNLOAD_URL=3D http://blast.w= ustl.edu/licensing=0AX=0AXNO_WRKSUBDIR=3D yes=0AXUSE_REINPLACE=3D yes=0AX= =0AXDOCS=3D COPYRIGHT FAQ-Indexing.html HISTORY LICENSE Memory.html \=0AX R= EADME.html parameters.html=0AXBINS=3D blasta gb2fasta gt2fasta memfile nrdb= pam patdb \=0AX pir2fasta sp2fasta xdformat xdget=0AXSCRIPTS=3D wu-blastal= l wu-formatdb=0AXBLASTA_LINKS=3D blastn blastp blastx tblastn tblastx=0AXXD= FORMAT_LINKS=3D setdb pressdb=0AX=0AX.include <bsd.port.pre.mk>=0AX=0AX.if = ${OSVERSION} < 500000=0AXDISTNAME=3D ${PORTNAME}${PORTVERSION:S/.0//}.freeb= sd-4.x-i686=0AX.else=0AXDISTNAME=3D ${PORTNAME}${PORTVERSION:S/.0//}.freebs= d-i686=0AX.endif=0AX=0AX.if !exists(${DISTDIR}/${DISTNAME}${EXTRACT_SUFX})= =0AXIGNORE=3D "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"=0AX.endif=0AX=0AXdo-install= :=0AX=0AX.for bin in ${BINS}=0AX ${INSTALL_PROGRAM} ${WRKSRC}/${bin} ${PREF= IX}/bin/=0AX.endfor=0AX=0AX.for script in ${SCRIPTS}=0AX ${INSTALL_SCRIPT} = ${WRKSRC}/${script} ${PREFIX}/bin/=0AX.endfor=0AX=0AX ${CHMOD} a-r ${PREFIX= }/bin/blasta=0AX=0AX.for blink in ${BLASTA_LINKS}=0AX @(cd ${PREFIX}/bin &&= ${LN} -s blasta ${blink} && ${CHOWN} -h ${BINOWN}:${BINGRP} ${blink})=0AX.= endfor=0AX=0AX.for xlink in ${XDFORMAT_LINKS}=0AX @(cd ${PREFIX}/bin && ${L= N} -s xdformat ${xlink} && ${CHOWN} -h ${BINOWN}:${BINGRP} ${xlink})=0AX.en= dfor=0AX=0AX.if !defined (NOPORTDOCS)=0AX @${MKDIR} ${DOCSDIR}=0AX=0AX.for = doc in ${DOCS}=0AX ${INSTALL_MAN} ${WRKSRC}/${doc} ${DOCSDIR}=0AX.endfor=0A= X=0AX.endif=0AX=0AX @${MKDIR} ${DATADIR}=0AX ${CP} -R ${WRKSRC}/matrix ${DA= TADIR}=0AX ${CP} -R ${WRKSRC}/filter ${DATADIR}=0AX ${CP} ${WRKSRC}/sysblas= t.sample ${DATADIR}=0AX=0AXpost-install:=0AX ${REINPLACE_CMD} -e 's,%%DATAD= IR%%,${DATADIR},g' ${PKGMESSAGE}=0AX @${CAT} ${PKGMESSAGE}.bak=0AX @${RM} $= {PKGMESSAGE}.bak=0AX=0AX.include <bsd.port.post.mk>=0AEND-of-blast/Makefile= =0Aecho x - blast/distinfo=0Ased 's/^X//' >blast/distinfo << 'END-of-blast/= distinfo'=0AXMD5 (blast2.freebsd-4.x-i686.tar.Z) =3D 3426153dc9fda4bddc0aff= 5b86c95a11=0AXMD5 (blast2.freebsd-i686.tar.Z) =3D 399e1fa6e275152e0a7642529= 09aa5b8=0AXSIZE (blast2.freebsd-4.x-i686.tar.Z) =3D 1555542=0AXSIZE (blast2= .freebsd-i686.tar.Z) =3D 1590385=0AEND-of-blast/distinfo=0Aecho x - blast/p= kg-message=0Ased 's/^X//' >blast/pkg-message << 'END-of-blast/pkg-message'= =0AX=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=0AX=0AXA= sample configuration file has been installed in /usr/tmp/share/blast and n= amed=0AXsysblast.sample. Edit it to suit your needs, rename it to 'sysblast= ' and=0AXplace it under /etc so that it can be recognized at runtime by the= blast=0AXexecutable.=0AX=0AXMatrix files and filter executables have been = placed in =0AX/usr/tmp/share/blast/matrix and /usr/tmp/share/blast/filter, = respectively. =0AXYou should set environment variables WUBLASTMAT and WUBLA= STFILTER=0AX(pointing to the respective directories) so that the blast exec= utable=0AXcan find them.=0AX=0AX=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=0AEND-of-blast/pkg-message=0Aecho x - blast/pkg-descr=0A= sed 's/^X//' >blast/pkg-descr << 'END-of-blast/pkg-descr'=0AXWashington Uni= versity BLAST (WU BLAST) version 2.0 is a powerful=0AXsoftware package for = gene and protein identification, using sensitive,=0AXselective and rapid si= milarity searches of protein and nucleotide=0AXsequence databases. WU BLAST= 2.0 builds upon WU BLAST 1.4, which in turn=0AXwas based on the public dom= ain NCBI BLAST version 1.4. While NCBI BLAST=0AXand WU BLAST 1.4 are in the= public domain, WU BLAST 2.0 contains=0AXsignificant new features and exten= ded capabilities, the development of=0AXwhich began in late 1994, at Washin= gton University in Saint Louis. First=0AXreleased in May 1996, or more than= a year ahead of the NCBI, WU BLAST=0AX2.0 is the original gapped BLAST wit= h statistics and is known for=0AXsetting higher standards for sensitivity, = speed, correctness and=0AXaccuracy, scalability and reliability than compet= ing programs and=0AXimplementations. WU BLAST is neither a re-hashed nor "M= ac-ified" version=0AXof NCBI BLAST, although WU BLAST in many ways is easie= r to use. WU BLAST=0AXessentially shares no code with NCBI BLAST, except fo= r portions that=0AXboth packages derived from ungapped NCBI BLAST 1.4.=0AX= =0AXWWW: http://blast.wustl.edu=0AEND-of-blast/pkg-descr=0Aecho x - blast/p= kg-plist=0Ased 's/^X//' >blast/pkg-plist << 'END-of-blast/pkg-plist'=0AXbin= /blasta=0AXbin/gb2fasta=0AXbin/gt2fasta=0AXbin/memfile=0AXbin/nrdb=0AXbin/p= am=0AXbin/patdb=0AXbin/pir2fasta=0AXbin/sp2fasta=0AXbin/xdformat=0AXbin/xdg= et=0AXbin/wu-blastall=0AXbin/wu-formatdb=0AXbin/blastn=0AXbin/blastp=0AXbin= /blastx=0AXbin/tblastn=0AXbin/tblastx=0AXbin/setdb=0AXbin/pressdb=0AXshare/= doc/blast/COPYRIGHT=0AXshare/doc/blast/FAQ-Indexing.html=0AXshare/doc/blast= /HISTORY=0AXshare/doc/blast/LICENSE=0AXshare/doc/blast/Memory.html=0AXshare= /doc/blast/README.html=0AXshare/doc/blast/parameters.html=0AXshare/blast/ma= trix/aa/nuc.4.4=0AXshare/blast/matrix/aa/BLOSUM30=0AXshare/blast/matrix/aa/= BLOSUM35=0AXshare/blast/matrix/aa/BLOSUM40=0AXshare/blast/matrix/aa/BLOSUM4= 5=0AXshare/blast/matrix/aa/BLOSUM50=0AXshare/blast/matrix/aa/BLOSUM55=0AXsh= are/blast/matrix/aa/BLOSUM60=0AXshare/blast/matrix/aa/BLOSUM62=0AXshare/bla= st/matrix/aa/BLOSUM65=0AXshare/blast/matrix/aa/BLOSUM70=0AXshare/blast/matr= ix/aa/BLOSUM75=0AXshare/blast/matrix/aa/BLOSUM80=0AXshare/blast/matrix/aa/B= LOSUM85=0AXshare/blast/matrix/aa/BLOSUM90=0AXshare/blast/matrix/aa/BLOSUMN= =0AXshare/blast/matrix/aa/blosum100=0AXshare/blast/matrix/aa/blosum30=0AXsh= are/blast/matrix/aa/blosum35=0AXshare/blast/matrix/aa/blosum40=0AXshare/bla= st/matrix/aa/blosum45=0AXshare/blast/matrix/aa/blosum50=0AXshare/blast/matr= ix/aa/blosum55=0AXshare/blast/matrix/aa/blosum60=0AXshare/blast/matrix/aa/b= losumn=0AXshare/blast/matrix/aa/blosum62=0AXshare/blast/matrix/aa/blosum65= =0AXshare/blast/matrix/aa/blosum70=0AXshare/blast/matrix/aa/blosum75=0AXsha= re/blast/matrix/aa/blosum80=0AXshare/blast/matrix/aa/blosum85=0AXshare/blas= t/matrix/aa/DAYHOFF=0AXshare/blast/matrix/aa/GONNET=0AXshare/blast/matrix/a= a/IDENTITY=0AXshare/blast/matrix/aa/MATCH=0AXshare/blast/matrix/aa/PAM10=0A= Xshare/blast/matrix/aa/NUC.4.2=0AXshare/blast/matrix/aa/NUC.4.4=0AXshare/bl= ast/matrix/aa/PAM100=0AXshare/blast/matrix/aa/PAM110=0AXshare/blast/matrix/= aa/PAM120=0AXshare/blast/matrix/aa/PAM130=0AXshare/blast/matrix/aa/PAM120.c= di=0AXshare/blast/matrix/aa/PAM140=0AXshare/blast/matrix/aa/PAM150=0AXshare= /blast/matrix/aa/PAM160=0AXshare/blast/matrix/aa/PAM170=0AXshare/blast/matr= ix/aa/PAM160.cdi=0AXshare/blast/matrix/aa/PAM180=0AXshare/blast/matrix/aa/P= AM190=0AXshare/blast/matrix/aa/PAM20=0AXshare/blast/matrix/aa/PAM200=0AXsha= re/blast/matrix/aa/PAM200.cdi=0AXshare/blast/matrix/aa/PAM210=0AXshare/blas= t/matrix/aa/PAM220=0AXshare/blast/matrix/aa/PAM230=0AXshare/blast/matrix/aa= /PAM240=0AXshare/blast/matrix/aa/PAM250=0AXshare/blast/matrix/aa/PAM250.cdi= =0AXshare/blast/matrix/aa/PAM260=0AXshare/blast/matrix/aa/PAM270=0AXshare/b= last/matrix/aa/PAM280=0AXshare/blast/matrix/aa/PAM290=0AXshare/blast/matrix= /aa/PAM30=0AXshare/blast/matrix/aa/PAM300=0AXshare/blast/matrix/aa/PAM310= =0AXshare/blast/matrix/aa/PAM320=0AXshare/blast/matrix/aa/PAM330=0AXshare/b= last/matrix/aa/PAM340=0AXshare/blast/matrix/aa/PAM350=0AXshare/blast/matrix= /aa/PAM360=0AXshare/blast/matrix/aa/PAM370=0AXshare/blast/matrix/aa/PAM380= =0AXshare/blast/matrix/aa/PAM390=0AXshare/blast/matrix/aa/PAM40=0AXshare/bl= ast/matrix/aa/PAM40.cdi=0AXshare/blast/matrix/aa/PAM400=0AXshare/blast/matr= ix/aa/PAM410=0AXshare/blast/matrix/aa/PAM420=0AXshare/blast/matrix/aa/PAM43= 0=0AXshare/blast/matrix/aa/PAM440=0AXshare/blast/matrix/aa/PAM450=0AXshare/= blast/matrix/aa/PAM460=0AXshare/blast/matrix/aa/PAM470=0AXshare/blast/matri= x/aa/PAM480=0AXshare/blast/matrix/aa/PAM490=0AXshare/blast/matrix/aa/PAM50= =0AXshare/blast/matrix/aa/PAM500=0AXshare/blast/matrix/aa/PAM60=0AXshare/bl= ast/matrix/aa/PAM70=0AXshare/blast/matrix/aa/PAM80=0AXshare/blast/matrix/aa= /PAM80.cdi=0AXshare/blast/matrix/aa/PAM90=0AXshare/blast/matrix/aa/blosum90= =0AXshare/blast/matrix/aa/pam120.cdi=0AXshare/blast/matrix/aa/pam160.cdi=0A= Xshare/blast/matrix/aa/dayhoff=0AXshare/blast/matrix/aa/gonnet=0AXshare/bla= st/matrix/aa/identity=0AXshare/blast/matrix/aa/match=0AXshare/blast/matrix/= aa/pam10=0AXshare/blast/matrix/aa/pam100=0AXshare/blast/matrix/aa/pam110=0A= Xshare/blast/matrix/aa/pam120=0AXshare/blast/matrix/aa/pam130=0AXshare/blas= t/matrix/aa/pam140=0AXshare/blast/matrix/aa/pam150=0AXshare/blast/matrix/aa= /pam160=0AXshare/blast/matrix/aa/pam170=0AXshare/blast/matrix/aa/pam180=0AX= share/blast/matrix/aa/pam190=0AXshare/blast/matrix/aa/pam20=0AXshare/blast/= matrix/aa/pam200=0AXshare/blast/matrix/aa/pam250.cdi=0AXshare/blast/matrix/= aa/pam210=0AXshare/blast/matrix/aa/pam220=0AXshare/blast/matrix/aa/pam230= =0AXshare/blast/matrix/aa/pam240=0AXshare/blast/matrix/aa/pam250=0AXshare/b= last/matrix/aa/pam40.cdi=0AXshare/blast/matrix/aa/pam260=0AXshare/blast/mat= rix/aa/pam270=0AXshare/blast/matrix/aa/pam280=0AXshare/blast/matrix/aa/pam2= 90=0AXshare/blast/matrix/aa/pam30=0AXshare/blast/matrix/aa/pam300=0AXshare/= blast/matrix/aa/pam310=0AXshare/blast/matrix/aa/pam320=0AXshare/blast/matri= x/aa/pam330=0AXshare/blast/matrix/aa/pam340=0AXshare/blast/matrix/aa/pam350= =0AXshare/blast/matrix/aa/pam360=0AXshare/blast/matrix/aa/pam370=0AXshare/b= last/matrix/aa/pam380=0AXshare/blast/matrix/aa/pam390=0AXshare/blast/matrix= /aa/pam40=0AXshare/blast/matrix/aa/pam80.cdi=0AXshare/blast/matrix/aa/pam40= 0=0AXshare/blast/matrix/aa/pam410=0AXshare/blast/matrix/aa/pam420=0AXshare/= blast/matrix/aa/pam430=0AXshare/blast/matrix/aa/pam440=0AXshare/blast/matri= x/aa/pam450=0AXshare/blast/matrix/aa/pam460=0AXshare/blast/matrix/aa/pam470= =0AXshare/blast/matrix/aa/pam480=0AXshare/blast/matrix/aa/pam490=0AXshare/b= last/matrix/aa/pam50=0AXshare/blast/matrix/aa/pam500=0AXshare/blast/matrix/= aa/pam60=0AXshare/blast/matrix/aa/pam70=0AXshare/blast/matrix/aa/pam80=0AXs= hare/blast/matrix/aa/pam90=0AXshare/blast/matrix/aa/pam200.cdi=0AXshare/bla= st/matrix/aa/PHAT_T70_B66=0AXshare/blast/matrix/aa/PHAT_T75_B73=0AXshare/bl= ast/matrix/aa/PHAT_T80_B78=0AXshare/blast/matrix/aa/PHAT_T85_B82=0AXshare/b= last/matrix/aa/phat_t70_b66=0AXshare/blast/matrix/aa/phat_t75_b73=0AXshare/= blast/matrix/aa/phat_t80_b78=0AXshare/blast/matrix/aa/phat_t85_b82=0AXshare= /blast/matrix/aa/nuc.4.2=0AXshare/blast/matrix/aa/BLOSUM100=0AXshare/blast/= matrix/nt/PUPY.4.4=0AXshare/blast/matrix/nt/IDENTITY.4.2=0AXshare/blast/mat= rix/nt/IDENTITY.4.4=0AXshare/blast/matrix/nt/identity.4.2=0AXshare/blast/ma= trix/nt/pupy.4.2=0AXshare/blast/matrix/nt/pupy.4.4=0AXshare/blast/matrix/nt= /PUPY.4.2=0AXshare/blast/matrix/nt/identity.4.4=0AXshare/blast/matrix/READM= E=0AXshare/blast/filter/seg=0AXshare/blast/filter/seg+xnu=0AXshare/blast/fi= lter/xnu+seg=0AXshare/blast/filter/nseg=0AXshare/blast/filter/dust=0AXshare= /blast/filter/nmerge=0AXshare/blast/filter/xnu=0AXshare/blast/filter/pmerge= =0AXshare/blast/filter/pseg=0AXshare/blast/filter/README=0AXshare/blast/sys= blast.sample=0AX@dirrm share/doc/blast=0AX@dirrm share/blast/matrix/aa=0AX@= dirrm share/blast/matrix/nt=0AX@dirrm share/blast/matrix=0AX@dirrm share/bl= ast/filter=0AX@dirrm share/blast=0AEND-of-blast/pkg-plist=0Aexit=0A=0A --0ntfKIWw70PvrIHh--
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