Date: Tue, 26 Feb 2002 15:02:22 +1100 (EST) From: Tony Maher <tonym@biolateral.com.au> To: FreeBSD-gnats-submit@freebsd.org Subject: ports/35330: New port: biology/wise Message-ID: <200202260402.g1Q42MS21827@yellow.biolateral.com.au>
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>Number: 35330 >Category: ports >Synopsis: New port: biology/wise >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Mon Feb 25 20:10:01 PST 2002 >Closed-Date: >Last-Modified: >Originator: Tony Maher >Release: FreeBSD 4.5-STABLE i386 >Organization: BioLateral >Environment: System: FreeBSD dt.home 4.5-STABLE FreeBSD 4.5-STABLE #0: Fri Feb 22 12:29:39 EST 2002 root@dt.home:/usr/obj/usr/src/sys/DT i386 >Description: New port: biology/wise "Wise2 is package that is focused on comparing DNA sequences at the level of its conceptual translation, regardless of sequencing error and introns." Licence is a mixture of BSD and GPL. The basic libs are BSD, some third party bundled apps are GPL. src/HMMer2/GNULICENSE src/base/LICENSE src/dyc/LICENSE src/dynlibsrc/LICENSE src/models/GNULICENSE The documentation is latex format (and does not compile without errors. For now I just install it raw in doc/wise but I hope to contact author with updated versions and get postscript versions included in tarball. The perl stuff is broken but this is added functionality that allows you to use base functionality in perl scripts. The actual applications are C based so this port is fully functional for a user (if not for perl developers which are likely to be a very very small minority). I will contact author to see if the perl problems can be fixed. portlint -Nact complains about possible use of absolute '/usr/local' in pkg-message but this is just a comment that only shows up when doing a binary pkg_add. >How-To-Repeat: >Fix: # 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: # # wise # wise/pkg-plist # wise/pkg-descr # wise/pkg-comment # wise/distinfo # wise/Makefile # wise/pkg-message # echo c - wise mkdir -p wise > /dev/null 2>&1 echo x - wise/pkg-plist sed 's/^X//' >wise/pkg-plist << 'END-of-wise/pkg-plist' X%%PORTDOCS%%share/doc/wise/README X%%PORTDOCS%%share/doc/wise/apiend.tex X%%PORTDOCS%%share/doc/wise/appendix.tex X%%PORTDOCS%%share/doc/wise/dynamite.tex X%%PORTDOCS%%share/doc/wise/genewise21.eps X%%PORTDOCS%%share/doc/wise/genewise6.eps X%%PORTDOCS%%share/doc/wise/gettex.pl X%%PORTDOCS%%share/doc/wise/makefile X%%PORTDOCS%%share/doc/wise/wise2.tex X%%PORTDOCS%%share/doc/wise/wise2api.tex X%%PORTDOCS%%share/doc/wise/wise3arch.tex X%%PORTDOCS%%share/examples/wise/README X%%PORTDOCS%%share/examples/wise/db.hmm X%%PORTDOCS%%share/examples/wise/hn_est.fa X%%PORTDOCS%%share/examples/wise/human.genomic X%%PORTDOCS%%share/examples/wise/keratin_intron.human X%%PORTDOCS%%share/examples/wise/keratin_intron.mouse X%%PORTDOCS%%share/examples/wise/pep.fa X%%PORTDOCS%%share/examples/wise/road.pep X%%PORTDOCS%%share/examples/wise/rrm.HMM X%%PORTDOCS%%share/examples/wise/vav.dna X%%PORTDOCS%%share/examples/wise/xeno.cdna X%%PORTDOCS%%share/examples/wise/xeno.pep Xshare/wise/BLOSUM30.bla Xshare/wise/BLOSUM45.bla Xshare/wise/BLOSUM62.bla Xshare/wise/BLOSUM80.bla Xshare/wise/aa.rnd Xshare/wise/blosum30.bla Xshare/wise/blosum62.bla Xshare/wise/cb.tmf Xshare/wise/codon.table Xshare/wise/gene.stat Xshare/wise/gon120.bla Xshare/wise/gon160.bla Xshare/wise/gon200.bla Xshare/wise/gon250.bla Xshare/wise/gon350.bla Xshare/wise/human.gf Xshare/wise/human.gp Xshare/wise/human.stats Xshare/wise/idenity.bla Xshare/wise/methods Xshare/wise/pb.gf Xshare/wise/pombe.gf Xshare/wise/tm.pri Xshare/wise/wise.2 Xshare/wise/wise.per Xshare/wise/worm.gf Xbin/dba Xbin/dnal Xbin/estwise Xbin/estwisedb Xbin/genewise Xbin/genewisedb Xbin/psw Xbin/pswdb X%%PORTDOCS%%@dirrm share/doc/wise X%%PORTDOCS%%@dirrm share/examples/wise X@dirrm share/wise END-of-wise/pkg-plist echo x - wise/pkg-descr sed 's/^X//' >wise/pkg-descr << 'END-of-wise/pkg-descr' X"Wise2 is package that is focused on comparing DNA sequences at Xthe level of its conceptual translation, regardless of sequencing Xerror and introns. This really is a rewrite of the old wisetools Xpackage, which I wrote about 3 years ago. X XIt can compare a single protein or a profile HMM to a genomic DNA Xsequence, and predict a gene structure. This is algorithm, called Xgenewise, is one of the algorithms available in Wise2. There are Xother algorithms focused on EST data rather than genomic data, as Xwell as some other algorithm curios." X- from the web site (Ewan Birney) X XWWW: http://www.sanger.ac.uk/Software/Wise2 END-of-wise/pkg-descr echo x - wise/pkg-comment sed 's/^X//' >wise/pkg-comment << 'END-of-wise/pkg-comment' XIntelligent algorithms for DNA searches END-of-wise/pkg-comment echo x - wise/distinfo sed 's/^X//' >wise/distinfo << 'END-of-wise/distinfo' XMD5 (wise2.2.0.tar.gz) = 0584240f77885e37528e99e64535ab60 END-of-wise/distinfo echo x - wise/Makefile sed 's/^X//' >wise/Makefile << 'END-of-wise/Makefile' X# New ports collection makefile for: wise X# Date created: 26 February 2002 X# Whom: Tony Maher <tonym@biolateral.com.au> X# X# $FreeBSD$ X# X XPORTNAME= wise XPORTVERSION= 2.2.0 XCATEGORIES= biology XMASTER_SITES= ftp://ftp.sanger.ac.uk/pub/birney/wise2/ XDISTNAME= ${PORTNAME}${PORTVERSION} X XMAINTAINER= tonym@biolateral.com.au X XWRKTOP= ${WRKDIR}/${DISTNAME} XWRKSRC= ${WRKTOP}/src XMAKEFILE= makefile X X# X# Actually want an 'ALL_TARGET = all perl' which then requires X# 'USE_PERL5= yes' but the perl sub-build is currently broken. X# The perl stuff is only so you can use the base libraries/functions X# from perl scripts. This is extra, independent functionality for the X# port and not required for the base system which are C applications. X# When the perl part is fixed, it will require an install line X# something like '@cd ${WRKSRC}/perl/Wise2; ${MAKE} install' X# X XBINFILES= dba dnal estwise estwisedb genewise genewisedb \ X genomewise psw pswdb XDATAFILES= BLOSUM30.bla BLOSUM45.bla BLOSUM62.bla BLOSUM80.bla \ X aa.rnd blosum30.bla blosum62.bla cb.tmf codon.table \ X gene.stat gon120.bla gon160.bla gon200.bla gon250.bla \ X gon350.bla human.gf human.gp human.stats idenity.bla \ X methods pb.gf pombe.gf tm.pri wise.2 wise.per worm.gf XDOCFILES= README apiend.tex appendix.tex dynamite.tex \ X genewise21.eps genewise6.eps gettex.pl makefile \ X wise2.tex wise2api.tex wise3arch.tex XEXFILES= README db.hmm hn_est.fa human.genomic \ X keratin_intron.human keratin_intron.mouse pep.fa \ X road.pep rrm.HMM vav.dna xeno.cdna xeno.pep X X# X# Top level makefile does not respect CFLAGS. Fixing it means X# having to fix some of the sub-directory makefiles. X# Note: some makefiles are ok and know that '-c' does not belong X# in CFLAGS and are part of the rule. X# X Xpost-configure: X @${PERL} -pi.orig \ X -e s'#^CFLAGS = -c -O#CFLAGS ?= -c -O#;' \ X -e s'#\tcsh welcome.csh##;' \ X ${WRKSRC}/${MAKEFILE} X @${PERL} -pi.orig \ X -e s'#CFLAGS\) $?#CFLAGS\) -c $?#;' \ X ${WRKSRC}/base/${MAKEFILE} X @${PERL} -pi.orig \ X -e s'#INCFLAGS\) $?#INCFLAGS\) -c $?#;' \ X ${WRKSRC}/dynlibsrc/${MAKEFILE} X @${PERL} -pi.orig \ X -e s'#INCFLAGS\) $?#INCFLAGS\) -c $?#;' \ X -e s'#CFLAGS\) estwise.c#CFLAGS\) -c estwise.c#;' \ X -e s'#CFLAGS\) estwiseb.c#CFLAGS\) -c estwiseb.c#;' \ X -e s'#CFLAGS\) estwisedb.c#CFLAGS\) -c estwisedb.c#;' \ X -e s'#CFLAGS\) genewise.c#CFLAGS\) -c genewise.c#;' \ X -e s'#CFLAGS\) genewisedb.c#CFLAGS\) -c genewisedb.c#;' \ X ${WRKSRC}/models/${MAKEFILE} X Xdo-install: X.for file in ${BINFILES} X @${INSTALL_PROGRAM} ${WRKSRC}/bin/${file} ${PREFIX}/bin X.endfor X @${MKDIR} ${DATADIR} X.for file in ${DATAFILES} X @${INSTALL_DATA} ${WRKTOP}/wisecfg/${file} ${DATADIR} X.endfor X.if !defined(NOPORTDOCS) X @${MKDIR} ${DOCSDIR} X.for file in ${DOCFILES} X @${INSTALL_DATA} ${WRKTOP}/docs/${file} ${DOCSDIR} X.endfor X @${MKDIR} ${EXAMPLESDIR} X.for file in ${EXFILES} X @${INSTALL_DATA} ${WRKTOP}/test_data/${file} ${EXAMPLESDIR} X.endfor X X.endif X Xpost-install: X @${SED} -E -e 's#PREFIX#${PREFIX}#' -e '/(^\[|]$$)/d' ${PKGMESSAGE} X X.include <bsd.port.mk> END-of-wise/Makefile echo x - wise/pkg-message sed 's/^X//' >wise/pkg-message << 'END-of-wise/pkg-message' XWelcome to Wise2.2 X XYou must set your WISECONFIGDIR to the config directory before Xusing the programs: X Xin (t)csh: setenv WISECONFIGDIR PREFIX/share/wise/ Xin (ba)sh: export WISECONFIGDIR=PREFIX/share/wise/ X XTo try an example: X Xcd PREFIX/share/examples/wise Xgenewise road.pep human.genomic X X[Replace 'PREFIX' above with the actual installation prefix, Xwhich by default is '/usr/local'.] END-of-wise/pkg-message exit >Release-Note: >Audit-Trail: >Unformatted: To Unsubscribe: send mail to majordomo@FreeBSD.org with "unsubscribe freebsd-ports" in the body of the message
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