Date: Fri, 28 Jul 2000 15:42:58 +0200 From: johann@egenetics.com To: FreeBSD-gnats-submit@freebsd.org Subject: ports/20252: New port: biology/p5-bioperl Message-ID: <E13IAPi-0006Nt-00@fling.sanbi.ac.za>
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>Number: 20252 >Category: ports >Synopsis: New port: biology/p5-bioperl >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: Fri Jul 28 06:50:00 PDT 2000 >Closed-Date: >Last-Modified: >Originator: Johann Visagie >Release: FreeBSD 3.5-STABLE i386 >Organization: Electric Genetics / SA National Bioinformatics Intsitute >Environment: FreeBSD fling.sanbi.ac.za 3.5-STABLE FreeBSD 3.5-STABLE #2: Fri Jul 14 17:30:00 SAST 2000 toor@fling.sanbi.ac.za:/usr/src/sys/compile/FLING i386 >Description: New port of Bioperl, a collection of Perl5 mods for bioinformatics/genomics. Depends on biology/p5-AcePerl which I submitted recently in ports/20223, and which has now been committed by nbm (thanks!) >How-To-Repeat: N/A >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: # # p5-bioperl # p5-bioperl/pkg # p5-bioperl/pkg/PLIST # p5-bioperl/pkg/DESCR # p5-bioperl/pkg/COMMENT # p5-bioperl/patches # p5-bioperl/patches/patch-aa # p5-bioperl/Makefile # p5-bioperl/files # p5-bioperl/files/md5 # echo c - p5-bioperl mkdir -p p5-bioperl > /dev/null 2>&1 echo c - p5-bioperl/pkg mkdir -p p5-bioperl/pkg > /dev/null 2>&1 echo x - p5-bioperl/pkg/PLIST sed 's/^X//' >p5-bioperl/pkg/PLIST << 'END-of-p5-bioperl/pkg/PLIST' Xlib/perl5/site_perl/%%PERL_VER%%/Bio/DB/GenBank.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/DB/SeqI.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/DB/Ace.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/DB/RandomAccessI.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/DB/GenPept.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Err.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Root/RootI.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Global.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Xref.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Object.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Vector.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Utilities.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Root/IOManager.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/RangeI.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/SeqI.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/UnivAln.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeatureI.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/genbank.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/FTHelper.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/raw.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/embl.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/scf.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/gcg.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/swiss.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/fasta.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/pir.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/MultiFile.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sim4/Results.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sim4/Exon.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/IUPAC.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/CodonTable.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/AlignFactory.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/Makefile.PL Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/postclient.pl Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/LocalBlast.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/Webblast.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/CHANGES Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/HSP.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Sbjct.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/README Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/HTML.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/pSW.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqPattern.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Fasta.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/WWW.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER/Results.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER/Set.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER/Domain.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sigcleave.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqWords.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqStats.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqAnal.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/RestrictionEnzyme.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/SearchDist.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit/HitI.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit/Fasta.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor/Fasta.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor/ProcessorI.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Result/ResultI.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Result/Fasta.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Seq.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/PrimarySeqI.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Range.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/SimpleAlign.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Index/EMBL.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Index/AbstractSeq.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Index/Fasta.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Index/Abstract.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Index/SwissPfam.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Species.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/PrimarySeq.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/LocatableSeq.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/Comment.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/Reference.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/DBLink.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/FeaturePair.pm Xlib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Generic.pm Xlib/perl5/site_perl/%%PERL_VER%%/bioperl.pod Xlib/perl5/site_perl/%%PERL_VER%%/bioback.pod Xlib/perl5/site_perl/%%PERL_VER%%/biodesign.pod Xlib/perl5/site_perl/%%PERL_VER%%/biostart.pod Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/.packlist Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/Align.bs Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/Align.so Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Bio/Ext/Align.pm Xlib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/.packlist X@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/DB X@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Root X@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO X@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sim4 X@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run X@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast X@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER X@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools X@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit X@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor X@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Result X@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search X@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Index X@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation X@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature X@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio X@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/ X@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext X@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio END-of-p5-bioperl/pkg/PLIST echo x - p5-bioperl/pkg/DESCR sed 's/^X//' >p5-bioperl/pkg/DESCR << 'END-of-p5-bioperl/pkg/DESCR' XThe Bioperl Project is an international association of developers of open Xsource Perl tools for bioinformatics, genomics and life science research. X XBioperl is a collection of object-oriented Perl modules created by the XBioperl Project. It forms the basis of a large number of bioinformatics and Xgenomics applications. X X(For an interesting aside on "How Perl saved the Human Genome Project", see Xhttp://bio.perl.org/GetStarted/tpj_ls_bio.html) X XWWW: http://bio.perl.org/ X X-- Johann Visagie <johann@egenetics.com> END-of-p5-bioperl/pkg/DESCR echo x - p5-bioperl/pkg/COMMENT sed 's/^X//' >p5-bioperl/pkg/COMMENT << 'END-of-p5-bioperl/pkg/COMMENT' XA collection of Perl modules for bioinformatics END-of-p5-bioperl/pkg/COMMENT echo c - p5-bioperl/patches mkdir -p p5-bioperl/patches > /dev/null 2>&1 echo x - p5-bioperl/patches/patch-aa sed 's/^X//' >p5-bioperl/patches/patch-aa << 'END-of-p5-bioperl/patches/patch-aa' X--- ../bioperl-ext-06/Bio/Ext/Align/libs/makefile.orig Thu Sep 16 15:33:08 1999 X+++ ../bioperl-ext-06/Bio/Ext/Align/libs/makefile Fri Jul 28 11:57:27 2000 X@@ -47,5 +47,5 @@ X # For NetBSD or Sun (solaris) installs, add -fPIC to the CFLAGS lines X # X X-CFLAGS = -c -O X+CFLAGS+= -c -O -fPIC X CC = cc END-of-p5-bioperl/patches/patch-aa echo x - p5-bioperl/Makefile sed 's/^X//' >p5-bioperl/Makefile << 'END-of-p5-bioperl/Makefile' X# New ports collection makefile for: p5-bioperl X# Date created: 28 July 2000 X# Whom: Johann Visagie <johann@egenetics.com> X# X# $FreeBSD$ X# X XPORTNAME= bioperl XPORTVERSION= 0.6.1 XCATEGORIES= biology perl5 XMASTER_SITES= ftp://bio.perl.org/pub/DIST/ \ X http://bio.perl.org/Core/Latest/ \ X ${MASTER_SITE_PERL_CPAN} XMASTER_SITE_SUBDIR=Bio XPKGNAMEPREFIX= p5- XDISTFILES= ${DISTNAME}${EXTRACT_SUFX} bioperl-ext-0.6.tar.gz X XMAINTAINER= johann@egenetics.com X XBUILD_DEPENDS= ${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/LWP/UserAgent.pm:${PORTSDIR}/www/p5-libwww \ X ${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/IO/Scalar.pm:${PORTSDIR}/devel/p5-IO-stringy \ X ${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/Ace.pm:${PORTSDIR}/biology/p5-AcePerl X XUSE_PERL5= YES X XEXT_WRKSRC= ${WRKDIR}/bioperl-ext-06 X XMAN3= Bio::Tools::CodonTable.3 \ X Bio::PrimarySeq.3 \ X Bio::Tools::SeqStats.3 \ X Bio::SimpleAlign.3 \ X Bio::Search::Processor::Fasta.3 \ X Bio::Root::Xref.3 \ X Bio::Annotation::DBLink.3 \ X Bio::SeqIO::swiss.3 \ X Bio::Annotation::Comment.3 \ X Bio::Tools::Sim4::Results.3 \ X Bio::Annotation::Reference.3 \ X Bio::SeqIO::pir.3 \ X Bio::Search::Hit::Fasta.3 \ X Bio::Tools::SeqAnal.3 \ X Bio::Annotation.3 \ X Bio::Tools::Blast::HTML.3 \ X Bio::Tools::HMMER::Results.3 \ X Bio::SeqIO::scf.3 \ X Bio::SeqIO::genbank.3 \ X Bio::Root::RootI.3 \ X Bio::Tools::SeqWords.3 \ X Bio::Root::Global.3 \ X Bio::Tools::pSW.3 \ X Bio::SeqIO::raw.3 \ X Bio::Tools::Blast::HSP.3 \ X bioperl.3 \ X Bio::RangeI.3 \ X Bio::Search::Processor.3 \ X Bio::Root::Object.3 \ X Bio::Tools::WWW.3 \ X Bio::PrimarySeqI.3 \ X Bio::Index::Abstract.3 \ X Bio::DB::Ace.3 \ X Bio::SeqFeature::Generic.3 \ X Bio::DB::SeqI.3 \ X Bio::Root::Vector.3 \ X Bio::Seq.3 \ X Bio::Range.3 \ X Bio::UnivAln.3 \ X Bio::Tools::Blast::Run::Webblast.3 \ X Bio::SeqIO::gcg.3 \ X biodesign.3 \ X Bio::Tools::RestrictionEnzyme.3 \ X Bio::DB::RandomAccessI.3 \ X biostart.3 \ X Bio::Tools::Sim4::Exon.3 \ X Bio::Search::Hit::HitI.3 \ X bioback.3 \ X Bio::Tools::HMMER::Domain.3 \ X Bio::SeqIO::FTHelper.3 \ X Bio::Root::IOManager.3 \ X Bio::LocatableSeq.3 \ X Bio::Index::AbstractSeq.3 \ X Bio::Tools::Fasta.3 \ X Bio::Tools::Blast::Sbjct.3 \ X Bio::Tools::IUPAC.3 \ X Bio::SeqIO.3 \ X Bio::SeqIO::MultiFile.3 \ X Bio::Tools::AlignFactory.3 \ X Bio::SeqIO::fasta.3 \ X Bio::SeqFeature::FeaturePair.3 \ X Bio::DB::GenBank.3 \ X Bio::SeqI.3 \ X Bio::Tools::Blast.3 \ X Bio::Tools::HMMER::Set.3 \ X Bio::SeqFeatureI.3 \ X Bio::SearchDist.3 \ X Bio::Tools::Sigcleave.3 \ X Bio::Search::Result::ResultI.3 \ X Bio::Root::Utilities.3 \ X Bio::Root::Err.3 \ X Bio::Search::Result::Fasta.3 \ X Bio::Tools::SeqPattern.3 \ X Bio::Search::Processor::ProcessorI.3 \ X Bio::Index::EMBL.3 \ X Bio::Species.3 \ X Bio::Tools::Blast::Run::LocalBlast.3 \ X Bio::SeqIO::embl.3 \ X Bio::Index::SwissPfam.3 \ X Bio::DB::GenPept.3 \ X Bio::Index::Fasta.3 X XMANPREFIX= ${PREFIX}/lib/perl5/${PERL_VERSION} X Xdo-configure: X @(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${PERL5} Makefile.PL) X @(cd ${EXT_WRKSRC}/Bio/Ext/Align; ${SETENV} ${MAKE_ENV} ${PERL5} Makefile.PL) X Xdo-build: X @(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET}) X @(cd ${EXT_WRKSRC}/Bio/Ext/Align; ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET}) X Xdo-install: X @(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${INSTALL_TARGET}) X @(cd ${EXT_WRKSRC}/Bio/Ext/Align; ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${INSTALL_TARGET}) X X.include <bsd.port.mk> END-of-p5-bioperl/Makefile echo c - p5-bioperl/files mkdir -p p5-bioperl/files > /dev/null 2>&1 echo x - p5-bioperl/files/md5 sed 's/^X//' >p5-bioperl/files/md5 << 'END-of-p5-bioperl/files/md5' XMD5 (bioperl-0.6.1.tar.gz) = e3506188027a94ea87443389a78c2fdc XMD5 (bioperl-ext-0.6.tar.gz) = 5bf87e0cf94d3d41fabbfd209971d240 END-of-p5-bioperl/files/md5 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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