Kwalitee Issues

buildtool_not_executable

Change the permissions of Build.PL/Makefile.PL to not-executable.

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-1.006900/lib/Bio/DB/SoapEUtilities/Result.pm -- Around line 137: You can't have =items (as at line 141) unless the first thing after the =over is an =item BioPerl-Run-1.006900/lib/Bio/Tools/Run/ERPIN.pm -- Around line 35: Non-ASCII character seen before =encoding in ''Ðumask'. Assuming CP1252

package_version_matches_dist_version

Fix the version(s).

use_warnings

Add 'use warnings' (or its equivalents) to all modules (this will require perl > 5.6), 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::DB::ESoap::WSDL, Bio::DB::SoapEUtilities, Bio::DB::SoapEUtilities::FetchAdaptor, Bio::DB::SoapEUtilities::FetchAdaptor::seq, Bio::DB::SoapEUtilities::FetchAdaptor::species, 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::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::Job, Bio::Tools::Run::Analysis::soap, Bio::Tools::Run::AnalysisFactory, Bio::Tools::Run::AnalysisFactory::soap, Bio::Tools::Run::AssemblerBase, Bio::Tools::Run::BEDTools, Bio::Tools::Run::BWA, Bio::Tools::Run::Bowtie, 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::MCS, Bio::Tools::Run::Maq, Bio::Tools::Run::Match, Bio::Tools::Run::Mdust, Bio::Tools::Run::Meme, Bio::Tools::Run::Minimo, Bio::Tools::Run::Newbler, 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::StandAloneBlastPlus, 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).

Modules

Name Abstract Version View
Bio::DB::ESoap Client for the NCBI Entrez EUtilities SOAP server 0 metacpan
Bio::DB::ESoap::WSDL WSDL parsing for Entrez SOAP EUtilities 0 metacpan
Bio::DB::SoapEUtilities Interface to the NCBI Entrez web service *BETA* 0 metacpan
Bio::DB::SoapEUtilities::DocSumAdaptor Handle for Entrez SOAP DocSums 0 metacpan
Bio::DB::SoapEUtilities::DocSumAdaptor::docsum 0 metacpan
Bio::DB::SoapEUtilities::FetchAdaptor Conversion of Entrez SOAP messages to BioPerl objects 0 metacpan
Bio::DB::SoapEUtilities::FetchAdaptor::seq Fetch adaptor for 'seq' efetch SOAP messages 0 metacpan
Bio::DB::SoapEUtilities::FetchAdaptor::species Fetch adaptor for 'taxonomy' efetch SOAP messages 0 metacpan
Bio::DB::SoapEUtilities::GQueryAdaptor Handle for Entrez SOAP GlobalQuery items 0 metacpan
Bio::DB::SoapEUtilities::GQueryAdaptor::gquery 0 metacpan
Bio::DB::SoapEUtilities::LinkAdaptor Handle for Entrez SOAP LinkSets 0 metacpan
Bio::DB::SoapEUtilities::LinkAdaptor::linkset 0 metacpan
Bio::DB::SoapEUtilities::Result Accessor object for SoapEUtilities results 0 metacpan
Bio::Factory::EMBOSS EMBOSS application factory class 0 metacpan
Bio::Installer::Clustalw DESCRIPTION of Object 0 metacpan
Bio::Installer::EMBOSS DESCRIPTION of Object 0 metacpan
Bio::Installer::Generic DESCRIPTION of Object 0 metacpan
Bio::Installer::Hyphy DESCRIPTION of Object 0 metacpan
Bio::Installer::Muscle DESCRIPTION of Object 0 metacpan
Bio::Installer::PAML DESCRIPTION of Object 0 metacpan
Bio::Installer::Probcons DESCRIPTION of Object 0 metacpan
Bio::Installer::SLR DESCRIPTION of Object 0 metacpan
Bio::Installer::TCoffee DESCRIPTION of Object 0 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 0 metacpan
Bio::Tools::Run::Alignment::Blat 0 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 0 metacpan
Bio::Tools::Run::Alignment::DBA Object for the alignment of two sequences using the DNA Block Aligner program. 0 metacpan
Bio::Tools::Run::Alignment::Exonerate 0 metacpan
Bio::Tools::Run::Alignment::Gmap Wrapper for running gmap. 0 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 0 metacpan
Bio::Tools::Run::Alignment::Lagan Object for the local execution of the LAGAN suite of tools (including MLAGAN for multiple sequence alignments) 0 metacpan
Bio::Tools::Run::Alignment::MAFFT run the MAFFT alignment tools 0 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 0 metacpan
Bio::Tools::Run::Alignment::Pal2Nal Wrapper for Pal2Nal 0 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 0 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 0 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. 0 metacpan
Bio::Tools::Run::Alignment::Sim4 Wrapper for Sim4 program that allows for alignment of cdna to genomic sequences 0 metacpan
Bio::Tools::Run::Alignment::StandAloneFasta Object for the local execution of the Fasta3 programs ((t)fasta3, (t)fastx3, (t)fasty3 ssearch3) 0 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 0 metacpan
Bio::Tools::Run::Analysis Module representing any (remote or local) analysis tool 0 metacpan
Bio::Tools::Run::Analysis::Job 0 metacpan
Bio::Tools::Run::Analysis::Job::soap 0 metacpan
Bio::Tools::Run::Analysis::Utils 0 metacpan
Bio::Tools::Run::Analysis::soap A SOAP-based access to the analysis tools 0 metacpan
Bio::Tools::Run::AnalysisFactory A directory of analysis tools 0 metacpan
Bio::Tools::Run::AnalysisFactory::soap A SOAP-based access to the list of analysis tools 0 metacpan
Bio::Tools::Run::AssemblerBase base class for wrapping external assemblers 0 metacpan
Bio::Tools::Run::BEDTools Run wrapper for the BEDTools suite of programs *BETA* 0 metacpan
Bio::Tools::Run::BEDTools::Config Configuration data for bowtie commands 0 metacpan
Bio::Tools::Run::BWA Run wrapper for the BWA short-read assembler *BETA* 0 metacpan
Bio::Tools::Run::BWA::Config Configuration data for BWA commands 0 metacpan
Bio::Tools::Run::BlastPlus A wrapper for NCBI's blast+ suite 0 metacpan
Bio::Tools::Run::BlastPlus::Config 0 metacpan
Bio::Tools::Run::Bowtie Run wrapper for the Bowtie short-read assembler *BETA* 0 metacpan
Bio::Tools::Run::Bowtie::Config Configuration data for bowtie commands 0 metacpan
Bio::Tools::Run::Cap3 wrapper for CAP3 0 metacpan
Bio::Tools::Run::Coil wrapper for ncoils program 0 metacpan
Bio::Tools::Run::EMBOSSApplication class for EMBOSS Applications 0 metacpan
Bio::Tools::Run::EMBOSSacd class for EMBOSS Application qualifiers 0 metacpan
Bio::Tools::Run::ERPIN Wrapper for local execution of the ERPIN suite of programs. 0 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. 0 metacpan
Bio::Tools::Run::Eponine Object for execution of the Eponine which is a mammalian TSS predictor 0 metacpan
Bio::Tools::Run::FootPrinter wrapper for the FootPrinter program 0 metacpan
Bio::Tools::Run::Genemark Wrapper for local execution of the GeneMark family of programs. 0 metacpan
Bio::Tools::Run::Genewise Object for predicting genes in a given sequence given a protein 0 metacpan
Bio::Tools::Run::Genscan Object for identifying genes in a given sequence given a matrix(for appropriate organisms). 0 metacpan
Bio::Tools::Run::Glimmer Wrapper for local execution of Glimmer, GlimmerM and GlimmerHMM. 0 metacpan
Bio::Tools::Run::Hmmer Wrapper for local execution of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam, hmmsearch 0 metacpan
Bio::Tools::Run::Infernal Wrapper for local execution of cmalign, cmbuild, cmsearch, cmscore 0 metacpan
Bio::Tools::Run::MCS Wrapper for MCS 0 metacpan
Bio::Tools::Run::Maq Run wrapper for the Maq short-read assembler *BETA* 0 metacpan
Bio::Tools::Run::Maq::Config Configuration data for maq commands 0 metacpan
Bio::Tools::Run::Match Wrapper for Transfac's match(TM) 0 metacpan
Bio::Tools::Run::Mdust 0 metacpan
Bio::Tools::Run::Meme Wrapper for Meme Program 0 metacpan
Bio::Tools::Run::Minimo Wrapper for local execution of the Minimo assembler 0 metacpan
Bio::Tools::Run::Newbler Wrapper for local execution of Newbler 0 metacpan
Bio::Tools::Run::Phrap a wrapper for running Phrap 0 metacpan
Bio::Tools::Run::Phylo::Gerp 0 metacpan
Bio::Tools::Run::Phylo::Gumby Wrapper for gumby 0 metacpan
Bio::Tools::Run::Phylo::Hyphy::Base Hyphy wrapping base methods 0 metacpan
Bio::Tools::Run::Phylo::Hyphy::FEL Wrapper around the Hyphy FEL analysis 0 metacpan
Bio::Tools::Run::Phylo::Hyphy::Modeltest Wrapper around the Hyphy Modeltest analysis 0 metacpan
Bio::Tools::Run::Phylo::Hyphy::REL Wrapper around the Hyphy REL analysis 0 metacpan
Bio::Tools::Run::Phylo::Hyphy::SLAC Wrapper around the Hyphy SLAC analysis 0 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. 0 metacpan
Bio::Tools::Run::Phylo::Molphy::ProtML A wrapper for the Molphy pkg app ProtML 0 metacpan
Bio::Tools::Run::Phylo::Njtree::Best Wrapper around the Njtree (Njtree/phyml) best program. 0 metacpan
Bio::Tools::Run::Phylo::PAML::Baseml Wrapper aroud the PAML program baseml 0 metacpan
Bio::Tools::Run::Phylo::PAML::Codeml Wrapper aroud the PAML program codeml 0 metacpan
Bio::Tools::Run::Phylo::PAML::Evolver Wrapper aroud the PAML program evolver 0 metacpan
Bio::Tools::Run::Phylo::PAML::Yn00 Wrapper aroud the PAML program yn00 0 metacpan
Bio::Tools::Run::Phylo::Phast::PhastCons Wrapper for footprinting using phastCons 0 metacpan
Bio::Tools::Run::Phylo::Phast::PhyloFit Wrapper for phyloFit 0 metacpan
Bio::Tools::Run::Phylo::Phylip::Base Base object for Phylip modules 0 metacpan
Bio::Tools::Run::Phylo::Phylip::Consense Wrapper for the phylip program Consense 0 metacpan
Bio::Tools::Run::Phylo::Phylip::DrawGram use Phylip DrawTree program to draw phylograms or phenograms 0 metacpan
Bio::Tools::Run::Phylo::Phylip::DrawTree use Phylip DrawTree program to draw trees 0 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. 0 metacpan
Bio::Tools::Run::Phylo::Phylip::PhylipConf 0 metacpan
Bio::Tools::Run::Phylo::Phylip::ProtDist Wrapper for the phylip program protdist 0 metacpan
Bio::Tools::Run::Phylo::Phylip::ProtPars Object for creating a L<Bio::Tree> object from a multiple alignment file or a SimpleAlign object 0 metacpan
Bio::Tools::Run::Phylo::Phylip::SeqBoot Wrapper for the phylip program SeqBoot 0 metacpan
Bio::Tools::Run::Phylo::PhyloBase 0 metacpan
Bio::Tools::Run::Phylo::Phyml Wrapper for rapid reconstruction of phylogenies using Phyml 0 metacpan
Bio::Tools::Run::Phylo::QuickTree Wrapper for rapid reconstruction of phylogenies using QuickTree 0 metacpan
Bio::Tools::Run::Phylo::SLR Wrapper around the SLR program 0 metacpan
Bio::Tools::Run::Phylo::Semphy Wrapper for Semphy 0 metacpan
Bio::Tools::Run::Primate 0 metacpan
Bio::Tools::Run::Primer3 Create input for and work with the output from the program primer3 0 metacpan
Bio::Tools::Run::Prints 0 metacpan
Bio::Tools::Run::Profile 0 metacpan
Bio::Tools::Run::Promoterwise Wrapper for aligning two sequences using promoterwise 0 metacpan
Bio::Tools::Run::Pseudowise Object for prediting pseudogenes in a given sequence given a protein and a cdna sequence 0 metacpan
Bio::Tools::Run::RNAMotif Wrapper for local execution of rnamotif, rm2ct, rmfmt, rmprune 0 metacpan
Bio::Tools::Run::RepeatMasker Wrapper for RepeatMasker Program 0 metacpan
Bio::Tools::Run::Samtools a run wrapper for the samtools suite *BETA* 0 metacpan
Bio::Tools::Run::Samtools::Config configurator for Bio::Tools::Run::Samtools 0 metacpan
Bio::Tools::Run::Seg Object for identifying low complexity regions in a given protein seequence. 0 metacpan
Bio::Tools::Run::Signalp 0 metacpan
Bio::Tools::Run::Simprot Wrapper around the Simprot program. Wrapper for the calculation of a multiple sequence alignment from a phylogenetic tree 0 metacpan
Bio::Tools::Run::StandAloneBlastPlus Compute with NCBI's blast+ suite *ALPHA* 0 metacpan
Bio::Tools::Run::TigrAssembler Wrapper for local execution of TIGR Assembler v2 0 metacpan
Bio::Tools::Run::Tmhmm Object for identifying transmembrane helixes in a given protein seequence. 0 metacpan
Bio::Tools::Run::TribeMCL 0 metacpan
Bio::Tools::Run::Vista 0 metacpan
Bio::Tools::Run::tRNAscanSE Wrapper for local execution of tRNAscan-SE 0 metacpan

Other Files

Build.PL metacpan
Changes metacpan
MANIFEST metacpan
META.json metacpan
META.yml metacpan
README metacpan