mirror of
https://git.FreeBSD.org/ports.git
synced 2024-11-24 00:45:52 +00:00
Add BioPerl, a collection of Perl5 mods for bioinformatics/genomics
PR: ports/20252 Submitted by: Johann Visagie <johann@egenetics.com>
This commit is contained in:
Neil Blakey-Milner
parent
167641b4f4
commit
4634742f54
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=31084
@ -12,6 +12,7 @@
|
||||
SUBDIR += mopac
|
||||
SUBDIR += ortep3
|
||||
SUBDIR += p5-AcePerl
|
||||
SUBDIR += p5-bioperl
|
||||
SUBDIR += paml
|
||||
SUBDIR += phylip
|
||||
SUBDIR += platon
|
||||
|
||||
124
biology/p5-bioperl/Makefile
Normal file
124
biology/p5-bioperl/Makefile
Normal file
@ -0,0 +1,124 @@
|
||||
# New ports collection makefile for: p5-bioperl
|
||||
# Date created: 28 July 2000
|
||||
# Whom: Johann Visagie <johann@egenetics.com>
|
||||
#
|
||||
# $FreeBSD$
|
||||
#
|
||||
|
||||
PORTNAME= bioperl
|
||||
PORTVERSION= 0.6.1
|
||||
CATEGORIES= biology perl5
|
||||
MASTER_SITES= ftp://bio.perl.org/pub/DIST/ \
|
||||
http://bio.perl.org/Core/Latest/ \
|
||||
${MASTER_SITE_PERL_CPAN}
|
||||
MASTER_SITE_SUBDIR=Bio
|
||||
PKGNAMEPREFIX= p5-
|
||||
DISTFILES= ${DISTNAME}${EXTRACT_SUFX} bioperl-ext-0.6.tar.gz
|
||||
|
||||
MAINTAINER= johann@egenetics.com
|
||||
|
||||
BUILD_DEPENDS= ${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/LWP/UserAgent.pm:${PORTSDIR}/www/p5-libwww \
|
||||
${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/IO/Scalar.pm:${PORTSDIR}/devel/p5-IO-stringy \
|
||||
${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/Ace.pm:${PORTSDIR}/biology/p5-AcePerl
|
||||
|
||||
USE_PERL5= YES
|
||||
|
||||
EXT_WRKSRC= ${WRKDIR}/bioperl-ext-06
|
||||
|
||||
MAN3= Bio::Tools::CodonTable.3 \
|
||||
Bio::PrimarySeq.3 \
|
||||
Bio::Tools::SeqStats.3 \
|
||||
Bio::SimpleAlign.3 \
|
||||
Bio::Search::Processor::Fasta.3 \
|
||||
Bio::Root::Xref.3 \
|
||||
Bio::Annotation::DBLink.3 \
|
||||
Bio::SeqIO::swiss.3 \
|
||||
Bio::Annotation::Comment.3 \
|
||||
Bio::Tools::Sim4::Results.3 \
|
||||
Bio::Annotation::Reference.3 \
|
||||
Bio::SeqIO::pir.3 \
|
||||
Bio::Search::Hit::Fasta.3 \
|
||||
Bio::Tools::SeqAnal.3 \
|
||||
Bio::Annotation.3 \
|
||||
Bio::Tools::Blast::HTML.3 \
|
||||
Bio::Tools::HMMER::Results.3 \
|
||||
Bio::SeqIO::scf.3 \
|
||||
Bio::SeqIO::genbank.3 \
|
||||
Bio::Root::RootI.3 \
|
||||
Bio::Tools::SeqWords.3 \
|
||||
Bio::Root::Global.3 \
|
||||
Bio::Tools::pSW.3 \
|
||||
Bio::SeqIO::raw.3 \
|
||||
Bio::Tools::Blast::HSP.3 \
|
||||
bioperl.3 \
|
||||
Bio::RangeI.3 \
|
||||
Bio::Search::Processor.3 \
|
||||
Bio::Root::Object.3 \
|
||||
Bio::Tools::WWW.3 \
|
||||
Bio::PrimarySeqI.3 \
|
||||
Bio::Index::Abstract.3 \
|
||||
Bio::DB::Ace.3 \
|
||||
Bio::SeqFeature::Generic.3 \
|
||||
Bio::DB::SeqI.3 \
|
||||
Bio::Root::Vector.3 \
|
||||
Bio::Seq.3 \
|
||||
Bio::Range.3 \
|
||||
Bio::UnivAln.3 \
|
||||
Bio::Tools::Blast::Run::Webblast.3 \
|
||||
Bio::SeqIO::gcg.3 \
|
||||
biodesign.3 \
|
||||
Bio::Tools::RestrictionEnzyme.3 \
|
||||
Bio::DB::RandomAccessI.3 \
|
||||
biostart.3 \
|
||||
Bio::Tools::Sim4::Exon.3 \
|
||||
Bio::Search::Hit::HitI.3 \
|
||||
bioback.3 \
|
||||
Bio::Tools::HMMER::Domain.3 \
|
||||
Bio::SeqIO::FTHelper.3 \
|
||||
Bio::Root::IOManager.3 \
|
||||
Bio::LocatableSeq.3 \
|
||||
Bio::Index::AbstractSeq.3 \
|
||||
Bio::Tools::Fasta.3 \
|
||||
Bio::Tools::Blast::Sbjct.3 \
|
||||
Bio::Tools::IUPAC.3 \
|
||||
Bio::SeqIO.3 \
|
||||
Bio::SeqIO::MultiFile.3 \
|
||||
Bio::Tools::AlignFactory.3 \
|
||||
Bio::SeqIO::fasta.3 \
|
||||
Bio::SeqFeature::FeaturePair.3 \
|
||||
Bio::DB::GenBank.3 \
|
||||
Bio::SeqI.3 \
|
||||
Bio::Tools::Blast.3 \
|
||||
Bio::Tools::HMMER::Set.3 \
|
||||
Bio::SeqFeatureI.3 \
|
||||
Bio::SearchDist.3 \
|
||||
Bio::Tools::Sigcleave.3 \
|
||||
Bio::Search::Result::ResultI.3 \
|
||||
Bio::Root::Utilities.3 \
|
||||
Bio::Root::Err.3 \
|
||||
Bio::Search::Result::Fasta.3 \
|
||||
Bio::Tools::SeqPattern.3 \
|
||||
Bio::Search::Processor::ProcessorI.3 \
|
||||
Bio::Index::EMBL.3 \
|
||||
Bio::Species.3 \
|
||||
Bio::Tools::Blast::Run::LocalBlast.3 \
|
||||
Bio::SeqIO::embl.3 \
|
||||
Bio::Index::SwissPfam.3 \
|
||||
Bio::DB::GenPept.3 \
|
||||
Bio::Index::Fasta.3
|
||||
|
||||
MANPREFIX= ${PREFIX}/lib/perl5/${PERL_VERSION}
|
||||
|
||||
do-configure:
|
||||
@(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${PERL5} Makefile.PL)
|
||||
@(cd ${EXT_WRKSRC}/Bio/Ext/Align; ${SETENV} ${MAKE_ENV} ${PERL5} Makefile.PL)
|
||||
|
||||
do-build:
|
||||
@(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET})
|
||||
@(cd ${EXT_WRKSRC}/Bio/Ext/Align; ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET})
|
||||
|
||||
do-install:
|
||||
@(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${INSTALL_TARGET})
|
||||
@(cd ${EXT_WRKSRC}/Bio/Ext/Align; ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${INSTALL_TARGET})
|
||||
|
||||
.include <bsd.port.mk>
|
||||
2
biology/p5-bioperl/distinfo
Normal file
2
biology/p5-bioperl/distinfo
Normal file
@ -0,0 +1,2 @@
|
||||
MD5 (bioperl-0.6.1.tar.gz) = e3506188027a94ea87443389a78c2fdc
|
||||
MD5 (bioperl-ext-0.6.tar.gz) = 5bf87e0cf94d3d41fabbfd209971d240
|
||||
9
biology/p5-bioperl/files/patch-aa
Normal file
9
biology/p5-bioperl/files/patch-aa
Normal file
@ -0,0 +1,9 @@
|
||||
--- ../bioperl-ext-06/Bio/Ext/Align/libs/makefile.orig Thu Sep 16 15:33:08 1999
|
||||
+++ ../bioperl-ext-06/Bio/Ext/Align/libs/makefile Fri Jul 28 11:57:27 2000
|
||||
@@ -47,5 +47,5 @@
|
||||
# For NetBSD or Sun (solaris) installs, add -fPIC to the CFLAGS lines
|
||||
#
|
||||
|
||||
-CFLAGS = -c -O
|
||||
+CFLAGS+= -c -O -fPIC
|
||||
CC = cc
|
||||
1
biology/p5-bioperl/pkg-comment
Normal file
1
biology/p5-bioperl/pkg-comment
Normal file
@ -0,0 +1 @@
|
||||
A collection of Perl modules for bioinformatics
|
||||
13
biology/p5-bioperl/pkg-descr
Normal file
13
biology/p5-bioperl/pkg-descr
Normal file
@ -0,0 +1,13 @@
|
||||
The Bioperl Project is an international association of developers of open
|
||||
source Perl tools for bioinformatics, genomics and life science research.
|
||||
|
||||
Bioperl is a collection of object-oriented Perl modules created by the
|
||||
Bioperl Project. It forms the basis of a large number of bioinformatics and
|
||||
genomics applications.
|
||||
|
||||
(For an interesting aside on "How Perl saved the Human Genome Project", see
|
||||
http://bio.perl.org/GetStarted/tpj_ls_bio.html)
|
||||
|
||||
WWW: http://bio.perl.org/
|
||||
|
||||
-- Johann Visagie <johann@egenetics.com>
|
||||
109
biology/p5-bioperl/pkg-plist
Normal file
109
biology/p5-bioperl/pkg-plist
Normal file
@ -0,0 +1,109 @@
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/GenBank.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/SeqI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/Ace.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/RandomAccessI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/GenPept.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Err.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/RootI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Global.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Xref.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Object.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Vector.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Utilities.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/IOManager.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/RangeI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/UnivAln.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeatureI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/genbank.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/FTHelper.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/raw.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/embl.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/scf.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/gcg.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/swiss.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/fasta.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/pir.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/MultiFile.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sim4/Results.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sim4/Exon.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/IUPAC.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/CodonTable.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/AlignFactory.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/Makefile.PL
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/postclient.pl
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/LocalBlast.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/Webblast.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/CHANGES
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/HSP.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Sbjct.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/README
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/HTML.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/pSW.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqPattern.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Fasta.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/WWW.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER/Results.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER/Set.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER/Domain.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sigcleave.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqWords.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqStats.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqAnal.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/RestrictionEnzyme.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SearchDist.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit/HitI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit/Fasta.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor/Fasta.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor/ProcessorI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Result/ResultI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Result/Fasta.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/PrimarySeqI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Range.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SimpleAlign.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/EMBL.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/AbstractSeq.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/Fasta.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/Abstract.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/SwissPfam.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Species.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/PrimarySeq.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/LocatableSeq.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/Comment.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/Reference.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/DBLink.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/FeaturePair.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Generic.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/bioperl.pod
|
||||
lib/perl5/site_perl/%%PERL_VER%%/bioback.pod
|
||||
lib/perl5/site_perl/%%PERL_VER%%/biodesign.pod
|
||||
lib/perl5/site_perl/%%PERL_VER%%/biostart.pod
|
||||
lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/.packlist
|
||||
lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/Align.bs
|
||||
lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/Align.so
|
||||
lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Bio/Ext/Align.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/.packlist
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/DB
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Root
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sim4
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Result
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Index
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio
|
||||
Loading…
Reference in New Issue
Block a user