- Released by
- CJFIELDS
- Version
- Release Date
- 2009-02-26
- Kwalitee
- 140.62
- Core Kwalitee
- 90.62
- LINKS
BioPerl-run 1.6.1 Deleted
Kwalitee Issues
- buildtool_not_executable
-
Change the permissions of Build.PL/Makefile.PL to not-executable.
- main_module_version_matches_dist_version
-
Make sure that the main module name and version are the same of the distribution.
- no_pod_errors
-
Remove the POD errors. You can check for POD errors automatically by including Test::Pod to your test suite.
Error: BioPerl-run-1.6.0/Bio/Tools/Run/ERPIN.pm -- Around line 35: Non-ASCII character seen before =encoding in ''Ãumask'. Assuming CP1252
- has_meta_json
-
Add a META.json to the distribution. Your buildtool should be able to autogenerate it.
- proper_libs
-
Move your *.pm files in a directory named 'lib'. The directory structure should look like 'lib/Your/Module.pm' for a module named 'Your::Module'. If you need to provide additional files, e.g. for testing, that should not be considered for Kwalitee, then you should look at the 'provides' map in META.yml to limit the files scanned; or use the 'no_index' map to exclude parts of the distribution.
Error: Bio/Factory/EMBOSS.pm, Bio/Installer/Clustalw.pm, Bio/Installer/EMBOSS.pm, Bio/Installer/Generic.pm, Bio/Installer/Hyphy.pm, Bio/Installer/Muscle.pm, Bio/Installer/PAML.pm, Bio/Installer/Probcons.pm, Bio/Installer/SLR.pm, Bio/Installer/TCoffee.pm, Bio/Tools/Run/Alignment/Amap.pm, Bio/Tools/Run/Alignment/Blat.pm, Bio/Tools/Run/Alignment/Clustalw.pm, Bio/Tools/Run/Alignment/DBA.pm, Bio/Tools/Run/Alignment/Exonerate.pm, Bio/Tools/Run/Alignment/Kalign.pm, Bio/Tools/Run/Alignment/Lagan.pm, Bio/Tools/Run/Alignment/MAFFT.pm, Bio/Tools/Run/Alignment/Muscle.pm, Bio/Tools/Run/Alignment/Pal2Nal.pm, Bio/Tools/Run/Alignment/Probalign.pm, Bio/Tools/Run/Alignment/Probcons.pm, Bio/Tools/Run/Alignment/Proda.pm, Bio/Tools/Run/Alignment/Sim4.pm, Bio/Tools/Run/Alignment/StandAloneFasta.pm, Bio/Tools/Run/Alignment/TCoffee.pm, Bio/Tools/Run/Analysis.pm, Bio/Tools/Run/Analysis.pm, Bio/Tools/Run/Analysis/soap.pm, Bio/Tools/Run/Analysis.pm, Bio/Tools/Run/Analysis/soap.pm, Bio/Tools/Run/AnalysisFactory.pm, Bio/Tools/Run/AnalysisFactory/soap.pm, Bio/Tools/Run/Cap3.pm, Bio/Tools/Run/Coil.pm, Bio/Tools/Run/EMBOSSApplication.pm, Bio/Tools/Run/EMBOSSacd.pm, Bio/Tools/Run/ERPIN.pm, Bio/Tools/Run/Ensembl.pm, Bio/Tools/Run/Eponine.pm, Bio/Tools/Run/FootPrinter.pm, Bio/Tools/Run/Genemark.pm, Bio/Tools/Run/Genewise.pm, Bio/Tools/Run/Genscan.pm, Bio/Tools/Run/Glimmer.pm, Bio/Tools/Run/Hmmer.pm, Bio/Tools/Run/Infernal.pm, Bio/Tools/Run/MCS.pm, Bio/Tools/Run/Match.pm, Bio/Tools/Run/Mdust.pm, Bio/Tools/Run/Meme.pm, Bio/Tools/Run/Phrap.pm, Bio/Tools/Run/Phylo/Gerp.pm, Bio/Tools/Run/Phylo/Gumby.pm, Bio/Tools/Run/Phylo/Hyphy/Base.pm, Bio/Tools/Run/Phylo/Hyphy/FEL.pm, Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm, Bio/Tools/Run/Phylo/Hyphy/REL.pm, Bio/Tools/Run/Phylo/Hyphy/SLAC.pm, Bio/Tools/Run/Phylo/LVB.pm, Bio/Tools/Run/Phylo/Molphy/ProtML.pm, Bio/Tools/Run/Phylo/Njtree/Best.pm, Bio/Tools/Run/Phylo/PAML/Baseml.pm, Bio/Tools/Run/Phylo/PAML/Codeml.pm, Bio/Tools/Run/Phylo/PAML/Evolver.pm, Bio/Tools/Run/Phylo/PAML/Yn00.pm, Bio/Tools/Run/Phylo/Phast/PhastCons.pm, Bio/Tools/Run/Phylo/Phast/PhyloFit.pm, Bio/Tools/Run/Phylo/Phylip/Base.pm, Bio/Tools/Run/Phylo/Phylip/Consense.pm, Bio/Tools/Run/Phylo/Phylip/DrawGram.pm, Bio/Tools/Run/Phylo/Phylip/DrawTree.pm, Bio/Tools/Run/Phylo/Phylip/Neighbor.pm, Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm, Bio/Tools/Run/Phylo/Phylip/ProtDist.pm, Bio/Tools/Run/Phylo/Phylip/ProtPars.pm, Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm, Bio/Tools/Run/Phylo/PhyloBase.pm, Bio/Tools/Run/Phylo/Phyml.pm, Bio/Tools/Run/Phylo/QuickTree.pm, Bio/Tools/Run/Phylo/SLR.pm, Bio/Tools/Run/Phylo/Semphy.pm, Bio/Tools/Run/Primate.pm, Bio/Tools/Run/Primer3.pm, Bio/Tools/Run/Prints.pm, Bio/Tools/Run/Profile.pm, Bio/Tools/Run/Promoterwise.pm, Bio/Tools/Run/Pseudowise.pm, Bio/Tools/Run/RNAMotif.pm, Bio/Tools/Run/RepeatMasker.pm, Bio/Tools/Run/Seg.pm, Bio/Tools/Run/Signalp.pm, Bio/Tools/Run/Simprot.pm, Bio/Tools/Run/TigrAssembler.pm, Bio/Tools/Run/Tmhmm.pm, Bio/Tools/Run/TribeMCL.pm, Bio/Tools/Run/Vista.pm, Bio/Tools/Run/tRNAscanSE.pm - use_warnings
-
Add 'use warnings' (or its equivalents) to all modules, or convince us that your favorite module is well-known enough and people can easily see the modules warn when something bad happens.
Error: Bio::Factory::EMBOSS, Bio::Installer::Clustalw, Bio::Installer::EMBOSS, Bio::Installer::Generic, Bio::Installer::Hyphy, Bio::Installer::Muscle, Bio::Installer::PAML, Bio::Installer::Probcons, Bio::Installer::SLR, Bio::Installer::TCoffee, Bio::Tools::Run::Alignment::Amap, Bio::Tools::Run::Alignment::Blat, Bio::Tools::Run::Alignment::Clustalw, Bio::Tools::Run::Alignment::DBA, Bio::Tools::Run::Alignment::Exonerate, Bio::Tools::Run::Alignment::Kalign, Bio::Tools::Run::Alignment::Lagan, Bio::Tools::Run::Alignment::MAFFT, Bio::Tools::Run::Alignment::Muscle, Bio::Tools::Run::Alignment::Pal2Nal, Bio::Tools::Run::Alignment::Probalign, Bio::Tools::Run::Alignment::Probcons, Bio::Tools::Run::Alignment::Proda, Bio::Tools::Run::Alignment::Sim4, Bio::Tools::Run::Alignment::StandAloneFasta, Bio::Tools::Run::Alignment::TCoffee, Bio::Tools::Run::Analysis, Bio::Tools::Run::Analysis::soap, Bio::Tools::Run::AnalysisFactory, Bio::Tools::Run::AnalysisFactory::soap, Bio::Tools::Run::Cap3, Bio::Tools::Run::Coil, Bio::Tools::Run::EMBOSSApplication, Bio::Tools::Run::EMBOSSacd, Bio::Tools::Run::ERPIN, Bio::Tools::Run::Ensembl, Bio::Tools::Run::Eponine, Bio::Tools::Run::FootPrinter, Bio::Tools::Run::Genewise, Bio::Tools::Run::Genscan, Bio::Tools::Run::Hmmer, Bio::Tools::Run::Infernal, Bio::Tools::Run::MCS, Bio::Tools::Run::Match, Bio::Tools::Run::Mdust, Bio::Tools::Run::Meme, Bio::Tools::Run::Phrap, Bio::Tools::Run::Phylo::Gerp, Bio::Tools::Run::Phylo::Gumby, Bio::Tools::Run::Phylo::Hyphy::Base, Bio::Tools::Run::Phylo::Hyphy::FEL, Bio::Tools::Run::Phylo::Hyphy::Modeltest, Bio::Tools::Run::Phylo::Hyphy::REL, Bio::Tools::Run::Phylo::Hyphy::SLAC, Bio::Tools::Run::Phylo::LVB, Bio::Tools::Run::Phylo::Molphy::ProtML, Bio::Tools::Run::Phylo::Njtree::Best, Bio::Tools::Run::Phylo::PAML::Baseml, Bio::Tools::Run::Phylo::PAML::Codeml, Bio::Tools::Run::Phylo::PAML::Evolver, Bio::Tools::Run::Phylo::PAML::Yn00, Bio::Tools::Run::Phylo::Phast::PhastCons, Bio::Tools::Run::Phylo::Phast::PhyloFit, Bio::Tools::Run::Phylo::Phylip::Base, Bio::Tools::Run::Phylo::Phylip::Consense, Bio::Tools::Run::Phylo::Phylip::DrawGram, Bio::Tools::Run::Phylo::Phylip::DrawTree, Bio::Tools::Run::Phylo::Phylip::Neighbor, Bio::Tools::Run::Phylo::Phylip::PhylipConf, Bio::Tools::Run::Phylo::Phylip::ProtDist, Bio::Tools::Run::Phylo::Phylip::ProtPars, Bio::Tools::Run::Phylo::Phylip::SeqBoot, Bio::Tools::Run::Phylo::PhyloBase, Bio::Tools::Run::Phylo::Phyml, Bio::Tools::Run::Phylo::QuickTree, Bio::Tools::Run::Phylo::SLR, Bio::Tools::Run::Phylo::Semphy, Bio::Tools::Run::Primate, Bio::Tools::Run::Primer3, Bio::Tools::Run::Prints, Bio::Tools::Run::Profile, Bio::Tools::Run::Promoterwise, Bio::Tools::Run::Pseudowise, Bio::Tools::Run::RNAMotif, Bio::Tools::Run::RepeatMasker, Bio::Tools::Run::Seg, Bio::Tools::Run::Signalp, Bio::Tools::Run::Simprot, Bio::Tools::Run::TigrAssembler, Bio::Tools::Run::Tmhmm, Bio::Tools::Run::TribeMCL, Bio::Tools::Run::Vista
- meta_yml_has_repository_resource
-
Add a 'repository' resource to the META.yml via 'meta_add' accessor (for Module::Build) or META_ADD parameter (for ExtUtils::MakeMaker).
- has_security_doc
-
Add SECURITY(.pod|md). See Software::Security::Policy.
- security_doc_contains_contact
-
Add SECURITY(.pod|md) and add a contact address. See Software::Security::Policy.
- has_contributing_doc
-
Add CONTRIBUTING(.pod|md). See https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/setting-guidelines-for-repository-contributors.
Modules
| Name | Abstract | Version | View |
|---|---|---|---|
| Bio::Factory::EMBOSS | EMBOSS application factory class | 1.006000 | metacpan |
| Bio::Installer::Clustalw | DESCRIPTION of Object | 1.006000 | metacpan |
| Bio::Installer::EMBOSS | DESCRIPTION of Object | 1.006000 | metacpan |
| Bio::Installer::Generic | DESCRIPTION of Object | 1.006000 | metacpan |
| Bio::Installer::Hyphy | DESCRIPTION of Object | 1.006000 | metacpan |
| Bio::Installer::Muscle | DESCRIPTION of Object | 1.006000 | metacpan |
| Bio::Installer::PAML | DESCRIPTION of Object | 1.006000 | metacpan |
| Bio::Installer::Probcons | DESCRIPTION of Object | 1.006000 | metacpan |
| Bio::Installer::SLR | DESCRIPTION of Object | 1.006000 | metacpan |
| Bio::Installer::TCoffee | DESCRIPTION of Object | 1.006000 | metacpan |
| Bio::Tools::Run::Alignment::Amap | Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the Amap (2.0) program | 1.006000 | metacpan |
| Bio::Tools::Run::Alignment::Blat | 1.006000 | metacpan | |
| Bio::Tools::Run::Alignment::Clustalw | Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Clustalw program | 1.006000 | metacpan |
| Bio::Tools::Run::Alignment::DBA | Object for the alignment of two sequences using the DNA Block Aligner program. | 1.006000 | metacpan |
| Bio::Tools::Run::Alignment::Exonerate | 1.006000 | metacpan | |
| Bio::Tools::Run::Alignment::Kalign | Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the KALIGN program | 1.006000 | metacpan |
| Bio::Tools::Run::Alignment::Lagan | Object for the local execution of the LAGAN suite of tools (including MLAGAN for multiple sequence alignments) | 1.006000 | metacpan |
| Bio::Tools::Run::Alignment::MAFFT | run the MAFFT alignment tools | 1.006000 | metacpan |
| Bio::Tools::Run::Alignment::Muscle | Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the MUSCLE program | 1.006000 | metacpan |
| Bio::Tools::Run::Alignment::Pal2Nal | Wrapper for Pal2Nal | 1.006000 | metacpan |
| Bio::Tools::Run::Alignment::Probalign | Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Probalign program | 1.006000 | metacpan |
| Bio::Tools::Run::Alignment::Probcons | Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the Probcons program | 1.006000 | metacpan |
| Bio::Tools::Run::Alignment::Proda | Object for the calculation of sets of multiple sequence alignments from a set of unaligned sequences or alignments using the Proda program. | 1.006000 | metacpan |
| Bio::Tools::Run::Alignment::Sim4 | Wrapper for Sim4 program that allows for alignment of cdna to genomic sequences | 1.006000 | metacpan |
| Bio::Tools::Run::Alignment::StandAloneFasta | Object for the local execution of the Fasta3 programs ((t)fasta3, (t)fastx3, (t)fasty3 ssearch3) | 1.006000 | metacpan |
| Bio::Tools::Run::Alignment::TCoffee | Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the TCoffee program | 1.006000 | metacpan |
| Bio::Tools::Run::Analysis | Module representing any (remote or local) analysis tool | 1.006000 | metacpan |
| Bio::Tools::Run::Analysis::Job | 1.006000 | metacpan | |
| Bio::Tools::Run::Analysis::Job::soap | 1.006000 | metacpan | |
| Bio::Tools::Run::Analysis::Utils | 1.006000 | metacpan | |
| Bio::Tools::Run::Analysis::soap | A SOAP-based access to the analysis tools | 1.006000 | metacpan |
| Bio::Tools::Run::AnalysisFactory | A directory of analysis tools | 1.006000 | metacpan |
| Bio::Tools::Run::AnalysisFactory::soap | A SOAP-based access to the list of analysis tools | 1.006000 | metacpan |
| Bio::Tools::Run::Cap3 | wrapper for Cap3 | 1.006000 | metacpan |
| Bio::Tools::Run::Coil | wrapper for ncoils program | 1.006000 | metacpan |
| Bio::Tools::Run::EMBOSSApplication | class for EMBOSS Applications | 1.006000 | metacpan |
| Bio::Tools::Run::EMBOSSacd | class for EMBOSS Application qualifiers | 1.006000 | metacpan |
| Bio::Tools::Run::ERPIN | Wrapper for local execution of the ERPIN suite of programs. | 1.006000 | metacpan |
| Bio::Tools::Run::Ensembl | A simplified front-end for setting up the registry for, and then using an Ensembl database with the Ensembl Perl API. | 1.006000 | metacpan |
| Bio::Tools::Run::Eponine | Object for execution of the Eponine which is a mammalian TSS predictor | 1.006000 | metacpan |
| Bio::Tools::Run::FootPrinter | wrapper for the FootPrinter program | 1.006000 | metacpan |
| Bio::Tools::Run::Genemark | Wrapper for local execution of the GeneMark family of programs. | 1.006000 | metacpan |
| Bio::Tools::Run::Genewise | Object for predicting genes in a given sequence given a protein | 1.006000 | metacpan |
| Bio::Tools::Run::Genscan | Object for identifying genes in a given sequence given a matrix(for appropriate organisms). | 1.006000 | metacpan |
| Bio::Tools::Run::Glimmer | Wrapper for local execution of Glimmer, GlimmerM and GlimmerHMM. | 1.006000 | metacpan |
| Bio::Tools::Run::Hmmer | Wrapper for local execution of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam, hmmsearch | 1.006000 | metacpan |
| Bio::Tools::Run::Infernal | Wrapper for local execution of cmalign, cmbuild, cmsearch, cmscore | 1.006000 | metacpan |
| Bio::Tools::Run::MCS | Wrapper for MCS | 1.006000 | metacpan |
| Bio::Tools::Run::Match | Wrapper for Transfac's match(TM) | 1.006000 | metacpan |
| Bio::Tools::Run::Mdust | 1.006000 | metacpan | |
| Bio::Tools::Run::Meme | Wrapper for Meme Program | 1.006000 | metacpan |
| Bio::Tools::Run::Phrap | a wrapper for running Phrap | 1.006000 | metacpan |
| Bio::Tools::Run::Phylo::Gerp | 1.006000 | metacpan | |
| Bio::Tools::Run::Phylo::Gumby | Wrapper for gumby | 1.006000 | metacpan |
| Bio::Tools::Run::Phylo::Hyphy::Base | Hyphy wrapping base methods | 1.006000 | metacpan |
| Bio::Tools::Run::Phylo::Hyphy::FEL | Wrapper around the Hyphy FEL analysis | 1.006000 | metacpan |
| Bio::Tools::Run::Phylo::Hyphy::Modeltest | Wrapper around the Hyphy Modeltest analysis | 1.006000 | metacpan |
| Bio::Tools::Run::Phylo::Hyphy::REL | Wrapper around the Hyphy REL analysis | 1.006000 | metacpan |
| Bio::Tools::Run::Phylo::Hyphy::SLAC | Wrapper around the Hyphy SLAC analysis | 1.006000 | metacpan |
| Bio::Tools::Run::Phylo::LVB | Object for using the LVB program to create an array of L<Bio::Tree> objects from a nucleotide multiple alignment file or a nucleotide SimpleAlign object. Works with LVB version 2.1. | 1.006000 | metacpan |
| Bio::Tools::Run::Phylo::Molphy::ProtML | A wrapper for the Molphy pkg app ProtML | 1.006000 | metacpan |
| Bio::Tools::Run::Phylo::Njtree::Best | Wrapper around the Njtree (Njtree/phyml) best program. | 1.006000 | metacpan |
| Bio::Tools::Run::Phylo::PAML::Baseml | Wrapper aroud the PAML program baseml | 1.006000 | metacpan |
| Bio::Tools::Run::Phylo::PAML::Codeml | Wrapper aroud the PAML program codeml | 1.006000 | metacpan |
| Bio::Tools::Run::Phylo::PAML::Evolver | Wrapper aroud the PAML program evolver | 1.006000 | metacpan |
| Bio::Tools::Run::Phylo::PAML::Yn00 | Wrapper aroud the PAML program yn00 | 1.006000 | metacpan |
| Bio::Tools::Run::Phylo::Phast::PhastCons | Wrapper for footprinting using phastCons | 1.006000 | metacpan |
| Bio::Tools::Run::Phylo::Phast::PhyloFit | Wrapper for phyloFit | 1.006000 | metacpan |
| Bio::Tools::Run::Phylo::Phylip::Base | Base object for Phylip modules | 1.006000 | metacpan |
| Bio::Tools::Run::Phylo::Phylip::Consense | Wrapper for the phylip program Consense | 1.006000 | metacpan |
| Bio::Tools::Run::Phylo::Phylip::DrawGram | use Phylip DrawTree program to draw phylograms or phenograms | 1.006000 | metacpan |
| Bio::Tools::Run::Phylo::Phylip::DrawTree | use Phylip DrawTree program to draw trees | 1.006000 | metacpan |
| Bio::Tools::Run::Phylo::Phylip::Neighbor | Wrapper for the phylip program neighbor by Joseph Felsenstein for creating a phylogenetic tree(either through Neighbor or UPGMA) based on protein distances based on amino substitution rate. | 1.006000 | metacpan |
| Bio::Tools::Run::Phylo::Phylip::PhylipConf | 1.006000 | metacpan | |
| Bio::Tools::Run::Phylo::Phylip::ProtDist | Wrapper for the phylip program protdist | 1.006000 | metacpan |
| Bio::Tools::Run::Phylo::Phylip::ProtPars | Object for creating a L<Bio::Tree> object from a multiple alignment file or a SimpleAlign object | 1.006000 | metacpan |
| Bio::Tools::Run::Phylo::Phylip::SeqBoot | Wrapper for the phylip program SeqBoot | 1.006000 | metacpan |
| Bio::Tools::Run::Phylo::PhyloBase | 1.006000 | metacpan | |
| Bio::Tools::Run::Phylo::Phyml | Wrapper for rapid reconstruction of phylogenies using Phyml | 1.006000 | metacpan |
| Bio::Tools::Run::Phylo::QuickTree | Wrapper for rapid reconstruction of phylogenies using QuickTree | 1.006000 | metacpan |
| Bio::Tools::Run::Phylo::SLR | Wrapper around the SLR program | 1.006000 | metacpan |
| Bio::Tools::Run::Phylo::Semphy | Wrapper for Semphy | 1.006000 | metacpan |
| Bio::Tools::Run::Primate | 1.006000 | metacpan | |
| Bio::Tools::Run::Primer3 | Create input for and work with the output from the program primer3 | 1.006000 | metacpan |
| Bio::Tools::Run::Prints | 1.006000 | metacpan | |
| Bio::Tools::Run::Profile | 1.006000 | metacpan | |
| Bio::Tools::Run::Promoterwise | Wrapper for aligning two sequences using promoterwise | 1.006000 | metacpan |
| Bio::Tools::Run::Pseudowise | Object for prediting pseudogenes in a given sequence given a protein and a cdna sequence | 1.006000 | metacpan |
| Bio::Tools::Run::RNAMotif | Wrapper for local execution of rnamotif, rm2ct, rmfmt, rmprune | 1.006000 | metacpan |
| Bio::Tools::Run::RepeatMasker | Wrapper for RepeatMasker Program | 1.006000 | metacpan |
| Bio::Tools::Run::Seg | Object for identifying low complexity regions in a given protein seequence. | 1.006000 | metacpan |
| Bio::Tools::Run::Signalp | 1.006000 | metacpan | |
| Bio::Tools::Run::Simprot | Wrapper around the Simprot program. Wrapper for the calculation of a multiple sequence alignment from a phylogenetic tree | 1.006000 | metacpan |
| Bio::Tools::Run::TigrAssembler | Wrapper for local execution of TIGR Assembler v2.0 | 1.006000 | metacpan |
| Bio::Tools::Run::Tmhmm | Object for identifying transmembrane helixes in a given protein seequence. | 1.006000 | metacpan |
| Bio::Tools::Run::TribeMCL | 1.006000 | metacpan | |
| Bio::Tools::Run::Vista | 1.006000 | metacpan | |
| Bio::Tools::Run::tRNAscanSE | Wrapper for local execution of tRNAscan-SE | 1.006000 | metacpan |
Other Files
| Build.PL | metacpan |
| Changes | metacpan |
| MANIFEST | metacpan |
| META.yml | metacpan |
| Makefile.PL | metacpan |
| README | metacpan |