BioPerl-Run 1.007000
- Released by
- CJFIELDS
- Version
- Release Date
- 2016-12-18
- Kwalitee
- 146.88
- Core Kwalitee
- 90.62
- LINKS
BioPerl-Run 1.007000
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-1.007000/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-1.007000/lib/Bio/Tools/Run/ERPIN.pm -- Around line 34: Non-ASCII character seen before =encoding in ''Ãumask'. Assuming CP1252
- 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::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::MSAProbs, 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::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::FastTree, Bio::Tools::Run::Phylo::Gerp, Bio::Tools::Run::Phylo::Gumby, Bio::Tools::Run::Phylo::Hyphy::Base, Bio::Tools::Run::Phylo::Hyphy::BatchFile, 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::Raxml, 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::StandAloneWUBlast, Bio::Tools::Run::TigrAssembler, Bio::Tools::Run::Tmhmm, Bio::Tools::Run::TribeMCL, Bio::Tools::Run::Vista, Bio::Tools::Run::WrapperBase
- 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 | metacpan | |
| Bio::DB::ESoap::WSDL | WSDL parsing for Entrez SOAP EUtilities | metacpan | |
| Bio::DB::SoapEUtilities | Interface to the NCBI Entrez web service *BETA* | metacpan | |
| Bio::DB::SoapEUtilities::DocSumAdaptor | Handle for Entrez SOAP DocSums | metacpan | |
| Bio::DB::SoapEUtilities::DocSumAdaptor::docsum | metacpan | ||
| Bio::DB::SoapEUtilities::FetchAdaptor | Conversion of Entrez SOAP messages to BioPerl objects | metacpan | |
| Bio::DB::SoapEUtilities::FetchAdaptor::seq | Fetch adaptor for 'seq' efetch SOAP messages | metacpan | |
| Bio::DB::SoapEUtilities::FetchAdaptor::species | Fetch adaptor for 'taxonomy' efetch SOAP messages | metacpan | |
| Bio::DB::SoapEUtilities::GQueryAdaptor | Handle for Entrez SOAP GlobalQuery items | metacpan | |
| Bio::DB::SoapEUtilities::GQueryAdaptor::gquery | metacpan | ||
| Bio::DB::SoapEUtilities::LinkAdaptor | Handle for Entrez SOAP LinkSets | metacpan | |
| Bio::DB::SoapEUtilities::LinkAdaptor::linkset | metacpan | ||
| Bio::DB::SoapEUtilities::Result | Accessor object for SoapEUtilities results | metacpan | |
| Bio::Factory::EMBOSS | EMBOSS application factory class | metacpan | |
| Bio::Installer::Clustalw | DESCRIPTION of Object | metacpan | |
| Bio::Installer::EMBOSS | DESCRIPTION of Object | metacpan | |
| Bio::Installer::Generic | DESCRIPTION of Object | metacpan | |
| Bio::Installer::Hyphy | DESCRIPTION of Object | metacpan | |
| Bio::Installer::Muscle | DESCRIPTION of Object | metacpan | |
| Bio::Installer::PAML | DESCRIPTION of Object | metacpan | |
| Bio::Installer::Probcons | DESCRIPTION of Object | metacpan | |
| Bio::Installer::SLR | DESCRIPTION of Object | metacpan | |
| Bio::Installer::TCoffee | DESCRIPTION of Object | 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 | metacpan | |
| Bio::Tools::Run::Alignment::Blat | 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 | metacpan | |
| Bio::Tools::Run::Alignment::DBA | Object for the alignment of two sequences using the DNA Block Aligner program. | metacpan | |
| Bio::Tools::Run::Alignment::Exonerate | metacpan | ||
| Bio::Tools::Run::Alignment::Gmap | Wrapper for running gmap. | 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 | metacpan | |
| Bio::Tools::Run::Alignment::Lagan | Object for the local execution of the LAGAN suite of tools (including MLAGAN for multiple sequence alignments) | metacpan | |
| Bio::Tools::Run::Alignment::MAFFT | run the MAFFT alignment tools | metacpan | |
| Bio::Tools::Run::Alignment::MSAProbs | Object for the calculation of a multiple sequence alignment (MSA) from a set of unaligned sequences using the MSAProbs program | 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 | metacpan | |
| Bio::Tools::Run::Alignment::Pal2Nal | Wrapper for Pal2Nal | 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 | 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 | 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. | metacpan | |
| Bio::Tools::Run::Alignment::Sim4 | Wrapper for Sim4 program that allows for alignment of cdna to genomic sequences | metacpan | |
| Bio::Tools::Run::Alignment::StandAloneFasta | Object for the local execution of the Fasta3 programs ((t)fasta3, (t)fastx3, (t)fasty3 ssearch3) | 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 | metacpan | |
| Bio::Tools::Run::Analysis | Module representing any (remote or local) analysis tool | metacpan | |
| Bio::Tools::Run::Analysis::Job | metacpan | ||
| Bio::Tools::Run::Analysis::Job::soap | metacpan | ||
| Bio::Tools::Run::Analysis::Utils | metacpan | ||
| Bio::Tools::Run::Analysis::soap | A SOAP-based access to the analysis tools | metacpan | |
| Bio::Tools::Run::AnalysisFactory | A directory of analysis tools | metacpan | |
| Bio::Tools::Run::AnalysisFactory::soap | A SOAP-based access to the list of analysis tools | metacpan | |
| Bio::Tools::Run::AssemblerBase | base class for wrapping external assemblers | metacpan | |
| Bio::Tools::Run::BEDTools | Run wrapper for the BEDTools suite of programs *BETA* | metacpan | |
| Bio::Tools::Run::BEDTools::Config | Configuration data for bowtie commands | metacpan | |
| Bio::Tools::Run::BWA | Run wrapper for the BWA short-read assembler *BETA* | metacpan | |
| Bio::Tools::Run::BWA::Config | Configuration data for BWA commands | metacpan | |
| Bio::Tools::Run::BlastPlus | A wrapper for NCBI's blast+ suite | metacpan | |
| Bio::Tools::Run::BlastPlus::Config | metacpan | ||
| Bio::Tools::Run::Bowtie | Run wrapper for the Bowtie short-read assembler *BETA* | metacpan | |
| Bio::Tools::Run::Bowtie::Config | Configuration data for bowtie commands | metacpan | |
| Bio::Tools::Run::Cap3 | wrapper for CAP3 | metacpan | |
| Bio::Tools::Run::Coil | wrapper for ncoils program | metacpan | |
| Bio::Tools::Run::EMBOSSApplication | class for EMBOSS Applications | metacpan | |
| Bio::Tools::Run::EMBOSSacd | class for EMBOSS Application qualifiers | metacpan | |
| Bio::Tools::Run::ERPIN | Wrapper for local execution of the ERPIN suite of programs. | 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. | metacpan | |
| Bio::Tools::Run::Eponine | Object for execution of the Eponine which is a mammalian TSS predictor | metacpan | |
| Bio::Tools::Run::FootPrinter | wrapper for the FootPrinter program | metacpan | |
| Bio::Tools::Run::Genemark | Wrapper for local execution of the GeneMark family of programs. | metacpan | |
| Bio::Tools::Run::Genewise | Object for predicting genes in a given sequence given a protein | metacpan | |
| Bio::Tools::Run::Genscan | Object for identifying genes in a given sequence given a matrix(for appropriate organisms). | metacpan | |
| Bio::Tools::Run::Glimmer | Wrapper for local execution of Glimmer, GlimmerM and GlimmerHMM. | metacpan | |
| Bio::Tools::Run::Hmmer | Wrapper for local execution of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam, hmmsearch | metacpan | |
| Bio::Tools::Run::Infernal | Wrapper for local execution of cmalign, cmbuild, cmsearch, cmscore | metacpan | |
| Bio::Tools::Run::MCS | Wrapper for MCS | metacpan | |
| Bio::Tools::Run::Maq | Run wrapper for the Maq short-read assembler *BETA* | metacpan | |
| Bio::Tools::Run::Maq::Config | Configuration data for maq commands | metacpan | |
| Bio::Tools::Run::Match | Wrapper for Transfac's match(TM) | metacpan | |
| Bio::Tools::Run::Mdust | metacpan | ||
| Bio::Tools::Run::Meme | Wrapper for Meme Program | metacpan | |
| Bio::Tools::Run::Minimo | Wrapper for local execution of the Minimo assembler | metacpan | |
| Bio::Tools::Run::Newbler | Wrapper for local execution of Newbler | metacpan | |
| Bio::Tools::Run::Phrap | a wrapper for running Phrap | metacpan | |
| Bio::Tools::Run::Phylo::FastTree | metacpan | ||
| Bio::Tools::Run::Phylo::Gerp | metacpan | ||
| Bio::Tools::Run::Phylo::Gumby | Wrapper for gumby | metacpan | |
| Bio::Tools::Run::Phylo::Hyphy::Base | Hyphy wrapping base methods | metacpan | |
| Bio::Tools::Run::Phylo::Hyphy::BatchFile | Wrapper for custom execution of Hyphy batch files | metacpan | |
| Bio::Tools::Run::Phylo::Hyphy::FEL | Wrapper around the Hyphy FEL analysis | metacpan | |
| Bio::Tools::Run::Phylo::Hyphy::Modeltest | Wrapper around the Hyphy Modeltest analysis | metacpan | |
| Bio::Tools::Run::Phylo::Hyphy::REL | Wrapper around the Hyphy REL analysis | metacpan | |
| Bio::Tools::Run::Phylo::Hyphy::SLAC | Wrapper around the Hyphy SLAC analysis | 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. | metacpan | |
| Bio::Tools::Run::Phylo::Molphy::ProtML | A wrapper for the Molphy pkg app ProtML | metacpan | |
| Bio::Tools::Run::Phylo::Njtree::Best | Wrapper around the Njtree (Njtree/phyml) best program. | metacpan | |
| Bio::Tools::Run::Phylo::PAML::Baseml | Wrapper aroud the PAML program baseml | metacpan | |
| Bio::Tools::Run::Phylo::PAML::Codeml | Wrapper aroud the PAML program codeml | metacpan | |
| Bio::Tools::Run::Phylo::PAML::Evolver | Wrapper aroud the PAML program evolver | metacpan | |
| Bio::Tools::Run::Phylo::PAML::Yn00 | Wrapper aroud the PAML program yn00 | metacpan | |
| Bio::Tools::Run::Phylo::Phast::PhastCons | Wrapper for footprinting using phastCons | metacpan | |
| Bio::Tools::Run::Phylo::Phast::PhyloFit | Wrapper for phyloFit | metacpan | |
| Bio::Tools::Run::Phylo::Phylip::Base | Base object for Phylip modules | metacpan | |
| Bio::Tools::Run::Phylo::Phylip::Consense | Wrapper for the phylip program Consense | metacpan | |
| Bio::Tools::Run::Phylo::Phylip::DrawGram | use Phylip DrawTree program to draw phylograms or phenograms | metacpan | |
| Bio::Tools::Run::Phylo::Phylip::DrawTree | use Phylip DrawTree program to draw trees | 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. | metacpan | |
| Bio::Tools::Run::Phylo::Phylip::PhylipConf | metacpan | ||
| Bio::Tools::Run::Phylo::Phylip::ProtDist | Wrapper for the phylip program protdist | metacpan | |
| Bio::Tools::Run::Phylo::Phylip::ProtPars | Object for creating a L<Bio::Tree> object from a multiple alignment file or a SimpleAlign object | metacpan | |
| Bio::Tools::Run::Phylo::Phylip::SeqBoot | Wrapper for the phylip program SeqBoot | metacpan | |
| Bio::Tools::Run::Phylo::PhyloBase | metacpan | ||
| Bio::Tools::Run::Phylo::Phyml | Wrapper for rapid reconstruction of phylogenies using Phyml | metacpan | |
| Bio::Tools::Run::Phylo::QuickTree | Wrapper for rapid reconstruction of phylogenies using QuickTree | metacpan | |
| Bio::Tools::Run::Phylo::Raxml | metacpan | ||
| Bio::Tools::Run::Phylo::SLR | Wrapper around the SLR program | metacpan | |
| Bio::Tools::Run::Phylo::Semphy | Wrapper for Semphy | metacpan | |
| Bio::Tools::Run::Primate | metacpan | ||
| Bio::Tools::Run::Primer3 | Create input for and work with the output from the program primer3 | metacpan | |
| Bio::Tools::Run::Prints | metacpan | ||
| Bio::Tools::Run::Profile | metacpan | ||
| Bio::Tools::Run::Promoterwise | Wrapper for aligning two sequences using promoterwise | metacpan | |
| Bio::Tools::Run::Pseudowise | Object for prediting pseudogenes in a given sequence given a protein and a cdna sequence | metacpan | |
| Bio::Tools::Run::RNAMotif | Wrapper for local execution of rnamotif, rm2ct, rmfmt, rmprune | metacpan | |
| Bio::Tools::Run::RepeatMasker | Wrapper for RepeatMasker Program | metacpan | |
| Bio::Tools::Run::Samtools | a run wrapper for the samtools suite *BETA* | metacpan | |
| Bio::Tools::Run::Samtools::Config | configurator for Bio::Tools::Run::Samtools | metacpan | |
| Bio::Tools::Run::Seg | Object for identifying low complexity regions in a given protein seequence. | metacpan | |
| Bio::Tools::Run::Signalp | metacpan | ||
| Bio::Tools::Run::Simprot | Wrapper around the Simprot program. Wrapper for the calculation of a multiple sequence alignment from a phylogenetic tree | metacpan | |
| Bio::Tools::Run::StandAloneBlast | Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). There is experimental support for WU-Blast and NCBI rpsblast. | metacpan | |
| Bio::Tools::Run::StandAloneBlastPlus | Compute with NCBI's blast+ suite *ALPHA* | metacpan | |
| Bio::Tools::Run::StandAloneNCBIBlast | Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). With experimental support for NCBI rpsblast. | metacpan | |
| Bio::Tools::Run::StandAloneWUBlast | Object for the local execution of WU-Blast. | metacpan | |
| Bio::Tools::Run::TigrAssembler | Wrapper for local execution of TIGR Assembler v2 | metacpan | |
| Bio::Tools::Run::Tmhmm | Object for identifying transmembrane helixes in a given protein seequence. | metacpan | |
| Bio::Tools::Run::TribeMCL | metacpan | ||
| Bio::Tools::Run::Vista | metacpan | ||
| Bio::Tools::Run::WrapperBase | A Base object for wrappers around executables | metacpan | |
| Bio::Tools::Run::tRNAscanSE | Wrapper for local execution of tRNAscan-SE | metacpan |