p5-Bio-MAGETAB contains the core MAGE-TAB Utilities Perl modules. This
is a beta release. All functions have now been implemented and most have test suites; the exceptions include the modules involved in export of MAGE-TAB documents, which are still a little experimental in nature. The API is mostly finalised (and fully documented), but some details may yet change where necessary to improve usability. WWW: http://search.cpan.org/dist/Bio-MAGETAB/ PR: ports/136021 Submitted by: Wen Heping <wenheping at gmail.com>
This commit is contained in:
Martin Wilke
parent
b531208a60
commit
5da99a81fe
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=236853
@ -61,6 +61,7 @@
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SUBDIR += p5-Bio-Das
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SUBDIR += p5-Bio-Glite
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SUBDIR += p5-Bio-Graphics
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SUBDIR += p5-Bio-MAGETAB
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SUBDIR += p5-Bio-Phylo
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SUBDIR += p5-bioperl
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SUBDIR += p5-bioperl-run
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96
biology/p5-Bio-MAGETAB/Makefile
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96
biology/p5-Bio-MAGETAB/Makefile
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@ -0,0 +1,96 @@
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# New ports collection makefile for: p5-Bio-MAGETAB
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# Date created: 23 June, 2009
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# Whom: Wen Heping <wenheping@gmail.com>
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#
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# $FreeBSD$
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#
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PORTNAME= Bio-MAGETAB
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PORTVERSION= 0.98
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CATEGORIES= biology perl5
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MASTER_SITES= CPAN
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PKGNAMEPREFIX= p5-
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MAINTAINER= wenheping@gmail.com
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COMMENT= A data model and utility API for the MAGE-TAB format
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BUILD_DEPENDS= p5-Test-Exception>=0.26:${PORTSDIR}/devel/p5-Test-Exception \
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p5-DateTime-Format-DateManip>=0.04:${PORTSDIR}/devel/p5-DateTime-Format-DateManip \
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p5-Moose-Policy>=0.03:${PORTSDIR}/devel/p5-Moose-Policy \
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p5-MooseX-Types>=0.10:${PORTSDIR}/devel/p5-MooseX-Types \
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p5-Parse-RecDescent>=1.96:${PORTSDIR}/devel/p5-Parse-RecDescent \
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p5-Params-Coerce>=0.14:${PORTSDIR}/devel/p5-Params-Coerce \
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p5-URI>=1.35:${PORTSDIR}/net/p5-URI \
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p5-Test-Exception>=0.26:${PORTSDIR}/devel/p5-Test-Exception \
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p5-Date-Manip>=5.44:${PORTSDIR}/devel/p5-Date-Manip \
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p5-DateTime>=0.43:${PORTSDIR}/devel/p5-DateTime \
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p5-Text-CSV_XS>=0.32:${PORTSDIR}/textproc/p5-Text-CSV_XS \
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p5-Email-Valid>=0.179:${PORTSDIR}/mail/p5-Email-Valid \
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p5-Moose>=0.43:${PORTSDIR}/devel/p5-Moose
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RUN_DEPENDS= ${BUILD_DEPENDS}
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PERL_CONFIGURE= YES
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MAN3= Bio::MAGETAB::Material.3 \
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Bio::MAGETAB::Types.3 \
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Bio::MAGETAB::ControlledTerm.3 \
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Bio::MAGETAB::Util::Reader::DataMatrix.3 \
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Bio::MAGETAB::DesignElement.3 \
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Bio::MAGETAB::Contact.3 \
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Bio::MAGETAB::Investigation.3 \
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Bio::MAGETAB::Comment.3 \
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Bio::MAGETAB::Sample.3 \
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Bio::MAGETAB::Publication.3 \
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Bio::MAGETAB::DataFile.3 \
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Bio::MAGETAB::Event.3 \
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Bio::MAGETAB::Edge.3 \
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Bio::MAGETAB::ArrayDesign.3 \
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Bio::MAGETAB.3 \
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Bio::MAGETAB::Util::Writer::ADF.3 \
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Bio::MAGETAB::MatrixColumn.3 \
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Bio::MAGETAB::Normalization.3 \
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Bio::MAGETAB::Util::Reader::TagValueFile.3 \
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Bio::MAGETAB::ParameterValue.3 \
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Bio::MAGETAB::Util::Reader::Tabfile.3 \
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Bio::MAGETAB::Util::Writer.3 \
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Bio::MAGETAB::Util::Writer::Tabfile.3 \
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Bio::MAGETAB::DataAcquisition.3 \
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Bio::MAGETAB::Util::Reader::SDRF.3 \
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Bio::MAGETAB::Assay.3 \
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Bio::MAGETAB::SDRFRow.3 \
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Bio::MAGETAB::Util::Writer::IDF.3 \
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Bio::MAGETAB::SDRF.3 \
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Bio::MAGETAB::MatrixRow.3 \
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Bio::MAGETAB::Data.3 \
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Bio::MAGETAB::Util::Reader.3 \
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Bio::MAGETAB::Extract.3 \
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Bio::MAGETAB::Util::Reader::IDF.3 \
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Bio::MAGETAB::TermSource.3 \
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Bio::MAGETAB::Measurement.3 \
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Bio::MAGETAB::Util::Builder.3 \
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Bio::MAGETAB::CompositeElement.3 \
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Bio::MAGETAB::Node.3 \
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Bio::MAGETAB::Util::DBLoader.3 \
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Bio::MAGETAB::BaseClass.3 \
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Bio::MAGETAB::Util::Writer::SDRF.3 \
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Bio::MAGETAB::Protocol.3 \
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Bio::MAGETAB::Reporter.3 \
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Bio::MAGETAB::Util::Reader::ADF.3 \
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Bio::MAGETAB::Factor.3 \
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Bio::MAGETAB::DatabaseEntry.3 \
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Bio::MAGETAB::Feature.3 \
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Bio::MAGETAB::LabeledExtract.3 \
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Bio::MAGETAB::ProtocolApplication.3 \
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Bio::MAGETAB::Util::RewriteAE.3 \
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Bio::MAGETAB::Source.3 \
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Bio::MAGETAB::Util::Persistence.3 \
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Bio::MAGETAB::Util::Writer::GraphViz.3 \
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Bio::MAGETAB::DataMatrix.3 \
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Bio::MAGETAB::FactorValue.3 \
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Bio::MAGETAB::ProtocolParameter.3
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post-extract:
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@${REINPLACE_CMD} -e 's?auto_install?#auto_install?g' \
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${WRKSRC}/Makefile.PL
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.include <bsd.port.mk>
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3
biology/p5-Bio-MAGETAB/distinfo
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3
biology/p5-Bio-MAGETAB/distinfo
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@ -0,0 +1,3 @@
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MD5 (Bio-MAGETAB-0.98.tar.gz) = 91ddd45bdbe836a9be1f09a7049bb98a
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SHA256 (Bio-MAGETAB-0.98.tar.gz) = 2a8bf1eb1883f9b9afa9c9caf2ebae74345fb3e0e1a1faf891f3790ebb223151
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SIZE (Bio-MAGETAB-0.98.tar.gz) = 240502
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8
biology/p5-Bio-MAGETAB/pkg-descr
Normal file
8
biology/p5-Bio-MAGETAB/pkg-descr
Normal file
@ -0,0 +1,8 @@
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p5-Bio-MAGETAB contains the core MAGE-TAB Utilities Perl modules. This
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is a beta release. All functions have now been implemented and most
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have test suites; the exceptions include the modules involved in
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export of MAGE-TAB documents, which are still a little experimental in
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nature. The API is mostly finalised (and fully documented), but some
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details may yet change where necessary to improve usability.
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WWW: http://search.cpan.org/dist/Bio-MAGETAB/
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69
biology/p5-Bio-MAGETAB/pkg-plist
Normal file
69
biology/p5-Bio-MAGETAB/pkg-plist
Normal file
@ -0,0 +1,69 @@
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bin/deploy_magetab_db.pl
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bin/fix_ae_magetab.pl
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bin/read_magetab.pl
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bin/unload_magetab_namespace.pl
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%%SITE_PERL%%/mach/auto/Bio/MAGETAB/.packlist
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%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/DataMatrix.pm
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%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/TagValueFile.pm
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%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/Tabfile.pm
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%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/SDRF.pm
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%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/IDF.pm
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%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/ADF.pm
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%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/ADF.pm
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%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/Tabfile.pm
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%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/IDF.pm
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%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/SDRF.pm
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%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/GraphViz.pm
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%%SITE_PERL%%/Bio/MAGETAB/Util/Writer.pm
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%%SITE_PERL%%/Bio/MAGETAB/Util/Reader.pm
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%%SITE_PERL%%/Bio/MAGETAB/Util/Builder.pm
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%%SITE_PERL%%/Bio/MAGETAB/Util/DBLoader.pm
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%%SITE_PERL%%/Bio/MAGETAB/Util/RewriteAE.pm
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%%SITE_PERL%%/Bio/MAGETAB/Util/Persistence.pm
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%%SITE_PERL%%/Bio/MAGETAB/Material.pm
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%%SITE_PERL%%/Bio/MAGETAB/Types.pm
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%%SITE_PERL%%/Bio/MAGETAB/ControlledTerm.pm
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%%SITE_PERL%%/Bio/MAGETAB/Contact.pm
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%%SITE_PERL%%/Bio/MAGETAB/DesignElement.pm
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%%SITE_PERL%%/Bio/MAGETAB/Investigation.pm
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%%SITE_PERL%%/Bio/MAGETAB/Comment.pm
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%%SITE_PERL%%/Bio/MAGETAB/Publication.pm
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%%SITE_PERL%%/Bio/MAGETAB/Sample.pm
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%%SITE_PERL%%/Bio/MAGETAB/DataFile.pm
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%%SITE_PERL%%/Bio/MAGETAB/ArrayDesign.pm
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%%SITE_PERL%%/Bio/MAGETAB/Event.pm
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%%SITE_PERL%%/Bio/MAGETAB/Edge.pm
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%%SITE_PERL%%/Bio/MAGETAB/MatrixColumn.pm
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%%SITE_PERL%%/Bio/MAGETAB/Normalization.pm
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%%SITE_PERL%%/Bio/MAGETAB/ParameterValue.pm
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%%SITE_PERL%%/Bio/MAGETAB/DataAcquisition.pm
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%%SITE_PERL%%/Bio/MAGETAB/Assay.pm
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%%SITE_PERL%%/Bio/MAGETAB/SDRFRow.pm
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%%SITE_PERL%%/Bio/MAGETAB/SDRF.pm
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%%SITE_PERL%%/Bio/MAGETAB/Data.pm
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%%SITE_PERL%%/Bio/MAGETAB/MatrixRow.pm
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%%SITE_PERL%%/Bio/MAGETAB/Extract.pm
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%%SITE_PERL%%/Bio/MAGETAB/Measurement.pm
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%%SITE_PERL%%/Bio/MAGETAB/TermSource.pm
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%%SITE_PERL%%/Bio/MAGETAB/CompositeElement.pm
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%%SITE_PERL%%/Bio/MAGETAB/BaseClass.pm
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%%SITE_PERL%%/Bio/MAGETAB/Node.pm
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%%SITE_PERL%%/Bio/MAGETAB/Protocol.pm
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%%SITE_PERL%%/Bio/MAGETAB/Reporter.pm
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%%SITE_PERL%%/Bio/MAGETAB/Factor.pm
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%%SITE_PERL%%/Bio/MAGETAB/ProtocolApplication.pm
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%%SITE_PERL%%/Bio/MAGETAB/LabeledExtract.pm
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%%SITE_PERL%%/Bio/MAGETAB/Feature.pm
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%%SITE_PERL%%/Bio/MAGETAB/DatabaseEntry.pm
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%%SITE_PERL%%/Bio/MAGETAB/Source.pm
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%%SITE_PERL%%/Bio/MAGETAB/ProtocolParameter.pm
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%%SITE_PERL%%/Bio/MAGETAB/FactorValue.pm
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%%SITE_PERL%%/Bio/MAGETAB/DataMatrix.pm
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%%SITE_PERL%%/Bio/MAGETAB.pm
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@dirrm %%SITE_PERL%%/mach/auto/Bio/MAGETAB
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@dirrmtry %%SITE_PERL%%/mach/auto/Bio
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@dirrm %%SITE_PERL%%/Bio/MAGETAB/Util/Reader
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@dirrm %%SITE_PERL%%/Bio/MAGETAB/Util/Writer
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@dirrm %%SITE_PERL%%/Bio/MAGETAB/Util
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@dirrm %%SITE_PERL%%/Bio/MAGETAB
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@dirrmtry %%SITE_PERL%%/Bio
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