BioPerl-Run

Metadata

Analyzed metadata and errors of BioPerl-Run.

{
   "abstracts_in_pod" : {
      "Bio::DB::ESoap" : "Client for the NCBI Entrez EUtilities SOAP server",
      "Bio::DB::ESoap::WSDL" : "WSDL parsing for Entrez SOAP EUtilities",
      "Bio::DB::SoapEUtilities" : "Interface to the NCBI Entrez web service *BETA*",
      "Bio::DB::SoapEUtilities::DocSumAdaptor" : "Handle for Entrez SOAP DocSums",
      "Bio::DB::SoapEUtilities::FetchAdaptor" : "Conversion of Entrez SOAP messages to BioPerl objects",
      "Bio::DB::SoapEUtilities::FetchAdaptor::seq" : "Fetch adaptor for 'seq'\nefetch SOAP messages",
      "Bio::DB::SoapEUtilities::FetchAdaptor::species" : "Fetch adaptor for\n'taxonomy' efetch SOAP messages",
      "Bio::DB::SoapEUtilities::GQueryAdaptor" : "Handle for Entrez SOAP GlobalQuery items",
      "Bio::DB::SoapEUtilities::LinkAdaptor" : "Handle for Entrez SOAP LinkSets",
      "Bio::DB::SoapEUtilities::Result" : "Accessor object for SoapEUtilities results",
      "Bio::Factory::EMBOSS" : "EMBOSS application factory class",
      "Bio::Installer::Clustalw" : "DESCRIPTION of Object",
      "Bio::Installer::EMBOSS" : "DESCRIPTION of Object",
      "Bio::Installer::Generic" : "DESCRIPTION of Object",
      "Bio::Installer::Hyphy" : "DESCRIPTION of Object",
      "Bio::Installer::Muscle" : "DESCRIPTION of Object",
      "Bio::Installer::PAML" : "DESCRIPTION of Object",
      "Bio::Installer::Probcons" : "DESCRIPTION of Object",
      "Bio::Installer::SLR" : "DESCRIPTION of Object",
      "Bio::Installer::TCoffee" : "DESCRIPTION of Object",
      "Bio::Tools::Run::Alignment::Amap" : "Object for the calculation of an\niterative multiple sequence alignment from a set of unaligned\nsequences or alignments using the Amap (2.0) program",
      "Bio::Tools::Run::Alignment::Clustalw" : "Object for the calculation of a\nmultiple sequence alignment from a set of unaligned sequences or\nalignments using the Clustalw program",
      "Bio::Tools::Run::Alignment::DBA" : "Object for the alignment of two\nsequences using the DNA Block Aligner program.",
      "Bio::Tools::Run::Alignment::Gmap" : "Wrapper for running gmap.",
      "Bio::Tools::Run::Alignment::Kalign" : "Object for the calculation of an\niterative multiple sequence alignment from a set of unaligned\nsequences or alignments using the KALIGN program",
      "Bio::Tools::Run::Alignment::Lagan" : "Object for the local execution of the LAGAN suite of tools (including MLAGAN for multiple sequence alignments)",
      "Bio::Tools::Run::Alignment::MAFFT" : "run the MAFFT alignment tools",
      "Bio::Tools::Run::Alignment::Muscle" : "Object for the calculation of an\niterative multiple sequence alignment from a set of unaligned\nsequences or alignments using the MUSCLE program",
      "Bio::Tools::Run::Alignment::Pal2Nal" : "Wrapper for Pal2Nal",
      "Bio::Tools::Run::Alignment::Probalign" : "Object for the calculation of\na multiple sequence alignment from a set of unaligned sequences or\nalignments using the Probalign program",
      "Bio::Tools::Run::Alignment::Probcons" : "Object for the calculation of an\niterative multiple sequence alignment from a set of unaligned\nsequences or alignments using the Probcons program",
      "Bio::Tools::Run::Alignment::Proda" : "Object for the calculation of sets\nof multiple sequence alignments from a set of unaligned sequences or\nalignments using the Proda program.",
      "Bio::Tools::Run::Alignment::Sim4" : "Wrapper for Sim4 program that allows\nfor alignment of cdna to genomic sequences",
      "Bio::Tools::Run::Alignment::StandAloneFasta" : "Object for the local\nexecution of the Fasta3 programs ((t)fasta3, (t)fastx3, (t)fasty3\nssearch3)",
      "Bio::Tools::Run::Alignment::TCoffee" : "Object for the calculation of a\nmultiple sequence alignment from a set of unaligned sequences or\nalignments using the TCoffee program",
      "Bio::Tools::Run::Analysis" : "Module representing any (remote or local)\nanalysis tool",
      "Bio::Tools::Run::Analysis::soap" : "A SOAP-based access to the analysis tools",
      "Bio::Tools::Run::AnalysisFactory" : "A directory of analysis tools",
      "Bio::Tools::Run::AnalysisFactory::soap" : "A SOAP-based access to the list of analysis tools",
      "Bio::Tools::Run::AssemblerBase" : "base class for wrapping external assemblers",
      "Bio::Tools::Run::BEDTools" : "Run wrapper for the BEDTools suite of programs *BETA*",
      "Bio::Tools::Run::BEDTools::Config" : "Configuration data for bowtie commands",
      "Bio::Tools::Run::BWA" : "Run wrapper for the BWA short-read assembler *BETA*",
      "Bio::Tools::Run::BWA::Config" : "Configuration data for BWA commands",
      "Bio::Tools::Run::BlastPlus" : "A wrapper for NCBI's blast+ suite",
      "Bio::Tools::Run::Bowtie" : "Run wrapper for the Bowtie short-read assembler *BETA*",
      "Bio::Tools::Run::Bowtie::Config" : "Configuration data for bowtie commands",
      "Bio::Tools::Run::Cap3" : "wrapper for CAP3",
      "Bio::Tools::Run::Coil" : "wrapper for ncoils program",
      "Bio::Tools::Run::EMBOSSApplication" : "class for EMBOSS Applications",
      "Bio::Tools::Run::EMBOSSacd" : "class for EMBOSS Application qualifiers",
      "Bio::Tools::Run::ERPIN" : "Wrapper for local execution of the ERPIN suite of\nprograms.",
      "Bio::Tools::Run::Ensembl" : "A simplified front-end for setting up the registry\n                           for, and then using an Ensembl database with the\n                           Ensembl Perl API.",
      "Bio::Tools::Run::Eponine" : "Object for execution of the Eponine which\nis a mammalian TSS predictor",
      "Bio::Tools::Run::FootPrinter" : "wrapper for the FootPrinter program",
      "Bio::Tools::Run::Genemark" : "Wrapper for local execution of the GeneMark\nfamily of programs.",
      "Bio::Tools::Run::Genewise" : "Object for predicting genes in a\ngiven sequence given a protein",
      "Bio::Tools::Run::Genscan" : "Object for identifying genes in a\ngiven sequence given a matrix(for appropriate organisms).",
      "Bio::Tools::Run::Gerp" : "Wrapper for GERP",
      "Bio::Tools::Run::Glimmer" : "Wrapper for local execution of Glimmer,\nGlimmerM and GlimmerHMM.",
      "Bio::Tools::Run::Hmmer" : "Wrapper for local execution of hmmalign, hmmbuild,\nhmmcalibrate, hmmemit, hmmpfam, hmmsearch",
      "Bio::Tools::Run::Infernal" : "Wrapper for local execution of cmalign, cmbuild,\ncmsearch, cmscore",
      "Bio::Tools::Run::MCS" : "Wrapper for MCS",
      "Bio::Tools::Run::Maq" : "Run wrapper for the Maq short-read assembler *BETA*",
      "Bio::Tools::Run::Maq::Config" : "Configuration data for maq commands",
      "Bio::Tools::Run::Match" : "Wrapper for Transfac's match(TM)",
      "Bio::Tools::Run::Meme" : "Wrapper for Meme Program",
      "Bio::Tools::Run::Minimo" : "Wrapper for local execution of the Minimo assembler",
      "Bio::Tools::Run::Newbler" : "Wrapper for local execution of Newbler",
      "Bio::Tools::Run::Phrap" : "a wrapper for running Phrap",
      "Bio::Tools::Run::Phylo::Gumby" : "Wrapper for gumby",
      "Bio::Tools::Run::Phylo::Hyphy::Base" : "Hyphy wrapping base methods",
      "Bio::Tools::Run::Phylo::Hyphy::FEL" : "Wrapper around the Hyphy FEL analysis",
      "Bio::Tools::Run::Phylo::Hyphy::Modeltest" : "Wrapper around the Hyphy Modeltest analysis",
      "Bio::Tools::Run::Phylo::Hyphy::REL" : "Wrapper around the Hyphy REL analysis",
      "Bio::Tools::Run::Phylo::Hyphy::SLAC" : "Wrapper around the Hyphy SLAC analysis",
      "Bio::Tools::Run::Phylo::LVB" : "Object for using the LVB program to create\nan array of L<Bio::Tree> objects from a nucleotide multiple alignment\nfile or a nucleotide SimpleAlign object. Works with LVB version 2.1.",
      "Bio::Tools::Run::Phylo::Molphy::ProtML" : "A wrapper for the Molphy pkg app ProtML",
      "Bio::Tools::Run::Phylo::Njtree::Best" : "Wrapper around the Njtree (Njtree/phyml) best program.",
      "Bio::Tools::Run::Phylo::PAML::Baseml" : "Wrapper aroud the PAML program baseml",
      "Bio::Tools::Run::Phylo::PAML::Codeml" : "Wrapper aroud the PAML program codeml",
      "Bio::Tools::Run::Phylo::PAML::Evolver" : "Wrapper aroud the PAML program evolver",
      "Bio::Tools::Run::Phylo::PAML::Yn00" : "Wrapper aroud the PAML program yn00",
      "Bio::Tools::Run::Phylo::Phast::PhastCons" : "Wrapper for footprinting using\n                                           phastCons",
      "Bio::Tools::Run::Phylo::Phast::PhyloFit" : "Wrapper for phyloFit",
      "Bio::Tools::Run::Phylo::Phylip::Base" : "Base object for Phylip modules",
      "Bio::Tools::Run::Phylo::Phylip::Consense" : "Wrapper for the phylip\nprogram Consense",
      "Bio::Tools::Run::Phylo::Phylip::DrawGram" : "use Phylip DrawTree program to draw phylograms or phenograms",
      "Bio::Tools::Run::Phylo::Phylip::DrawTree" : "use Phylip DrawTree \nprogram to draw trees",
      "Bio::Tools::Run::Phylo::Phylip::Neighbor" : "Wrapper for the phylip\nprogram neighbor by Joseph Felsenstein for creating a phylogenetic\ntree(either through Neighbor or UPGMA) based on protein distances\nbased on amino substitution rate.",
      "Bio::Tools::Run::Phylo::Phylip::ProtDist" : "Wrapper for the phylip\nprogram protdist",
      "Bio::Tools::Run::Phylo::Phylip::ProtPars" : "Object for creating a L<Bio::Tree> object from a multiple alignment file or a SimpleAlign object",
      "Bio::Tools::Run::Phylo::Phylip::SeqBoot" : "Wrapper for the phylip\nprogram SeqBoot",
      "Bio::Tools::Run::Phylo::Phyml" : "Wrapper for rapid reconstruction of phylogenies using Phyml",
      "Bio::Tools::Run::Phylo::QuickTree" : "Wrapper for rapid reconstruction of\n                                    phylogenies using QuickTree",
      "Bio::Tools::Run::Phylo::SLR" : "Wrapper around the SLR program",
      "Bio::Tools::Run::Phylo::Semphy" : "Wrapper for Semphy",
      "Bio::Tools::Run::Primer3" : "Create input for and work with the output \nfrom the program primer3",
      "Bio::Tools::Run::Promoterwise" : "Wrapper for aligning two sequences using\npromoterwise",
      "Bio::Tools::Run::Pseudowise" : "Object for prediting pseudogenes in a\ngiven sequence given a protein and a cdna sequence",
      "Bio::Tools::Run::RNAMotif" : "Wrapper for local execution of rnamotif, rm2ct,\nrmfmt, rmprune",
      "Bio::Tools::Run::RepeatMasker" : "Wrapper for RepeatMasker Program",
      "Bio::Tools::Run::Samtools" : "a run wrapper for the samtools suite *BETA*",
      "Bio::Tools::Run::Samtools::Config" : "configurator for Bio::Tools::Run::Samtools",
      "Bio::Tools::Run::Seg" : "Object for identifying low complexity\n  regions in a given protein seequence.",
      "Bio::Tools::Run::Simprot" : "Wrapper around the Simprot program. Wrapper for the calculation of a multiple sequence alignment from a phylogenetic tree",
      "Bio::Tools::Run::StandAloneBlastPlus" : "Compute with NCBI's blast+ suite *ALPHA*",
      "Bio::Tools::Run::TigrAssembler" : "Wrapper for local execution of TIGR Assembler\n v2",
      "Bio::Tools::Run::Tmhmm" : "Object for identifying transmembrane helixes\n  in a given protein seequence.",
      "Bio::Tools::Run::tRNAscanSE" : "Wrapper for local execution of tRNAscan-SE",
      "Mdust" : "Perl extension for Mdust nucleotide filtering ",
      "annotation" : "either a file or and array ref of Bio::SeqFeatureI\n                             indicating the exons\n                regmin     -region min"
   },
   "author" : "CJFIELDS",
   "buildfile_executable" : 2,
   "dir_lib" : "lib",
   "dir_t" : "t",
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      "lib/Bio/DB/ESoap",
      "lib/Bio/DB/SoapEUtilities/FetchAdaptor",
      "lib/Bio/DB/SoapEUtilities",
      "lib/Bio/DB",
      "lib/Bio/Factory",
      "lib/Bio/Installer",
      "lib/Bio/Tools/Run/Alignment",
      "lib/Bio/Tools/Run/Analysis",
      "lib/Bio/Tools/Run/AnalysisFactory",
      "lib/Bio/Tools/Run/BEDTools",
      "lib/Bio/Tools/Run/BWA",
      "lib/Bio/Tools/Run/BlastPlus",
      "lib/Bio/Tools/Run/Bowtie",
      "lib/Bio/Tools/Run/Maq",
      "lib/Bio/Tools/Run/Phylo/Hyphy",
      "lib/Bio/Tools/Run/Phylo/Molphy",
      "lib/Bio/Tools/Run/Phylo/Njtree",
      "lib/Bio/Tools/Run/Phylo/PAML",
      "lib/Bio/Tools/Run/Phylo/Phast",
      "lib/Bio/Tools/Run/Phylo/Phylip",
      "lib/Bio/Tools/Run/Phylo",
      "lib/Bio/Tools/Run/Samtools",
      "lib/Bio/Tools/Run/StandAloneBlastPlus",
      "lib/Bio/Tools/Run",
      "lib/Bio/Tools",
      "lib/Bio",
      "lib",
      "scripts",
      "t/data/bowtie/indexes",
      "t/data/bowtie/reads",
      "t/data/bowtie",
      "t/data/gerp",
      "t/data/gumby",
      "t/data/taxdump",
      "t/data",
      "t/lib/Sub",
      "t/lib/Test/Builder",
      "t/lib/Test/Harness",
      "t/lib/Test",
      "t/lib",
      "t",
      "t"
   ],
   "dist" : "BioPerl-Run",
   "dynamic_config" : 1,
   "error" : {
      "no_pod_errors" : "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 ''√źumask'. Assuming  ISO8859-1",
      "use_warnings" : "Bio::Tools::Run::Phylo::Hyphy::Base, Bio::Tools::Run::Phylo::Gumby, Bio::Tools::Run::Bowtie, Bio::Installer::TCoffee, Bio::Tools::Run::Phylo::PAML::Evolver, Bio::Tools::Run::Meme, Bio::Tools::Run::Phylo::Phylip::Neighbor, Bio::Tools::Run::Seg, Bio::Tools::Run::Alignment::Probcons, Bio::Installer::Hyphy, Bio::Tools::Run::Newbler, Bio::Tools::Run::Hmmer, Bio::Tools::Run::Phylo::Phylip::DrawGram, Bio::Tools::Run::BWA, Bio::Tools::Run::Vista, Bio::Tools::Run::BEDTools, Bio::Tools::Run::Phylo::Phyml, Bio::Tools::Run::Phylo::PAML::Codeml, Bio::Tools::Run::Phylo::Njtree::Best, Bio::Tools::Run::Phylo::Hyphy::FEL, Bio::Tools::Run::Phrap, Bio::DB::SoapEUtilities::FetchAdaptor::seq, Bio::Tools::Run::Phylo::PAML::Baseml, Bio::Tools::Run::Signalp, Bio::Tools::Run::TribeMCL, Bio::Tools::Run::Cap3, Bio::Tools::Run::Alignment::StandAloneFasta, Bio::Tools::Run::Phylo::SLR, Bio::Tools::Run::Genewise, Bio::Tools::Run::Phylo::Phylip::ProtPars, Bio::Tools::Run::Coil, Bio::DB::SoapEUtilities::FetchAdaptor, Bio::Tools::Run::FootPrinter, Bio::Tools::Run::Minimo, Bio::Tools::Run::Phylo::Phylip::SeqBoot, Bio::Tools::Run::Analysis::soap, Bio::Tools::Run::Pseudowise, Bio::Tools::Run::Phylo::PAML::Yn00, Bio::Tools::Run::Prints, Bio::Tools::Run::Eponine, Bio::Tools::Run::RNAMotif, Bio::Tools::Run::EMBOSSacd, Bio::Tools::Run::Phylo::LVB, Bio::Tools::Run::Alignment::Clustalw, Bio::Tools::Run::Phylo::Phast::PhastCons, Bio::Tools::Run::Mdust, Bio::Tools::Run::AnalysisFactory::soap, Bio::Tools::Run::Tmhmm, Bio::Tools::Run::Alignment::Lagan, Bio::Installer::Muscle, Bio::Tools::Run::Phylo::Hyphy::REL, Bio::Tools::Run::Phylo::Gerp, Bio::DB::SoapEUtilities::FetchAdaptor::species, Bio::Tools::Run::AnalysisFactory, Bio::Tools::Run::RepeatMasker, Bio::Tools::Run::Alignment::Sim4, Bio::Tools::Run::AssemblerBase, Bio::DB::SoapEUtilities, Bio::Tools::Run::MCS, Bio::Tools::Run::Phylo::Hyphy::SLAC, Bio::Tools::Run::StandAloneBlastPlus, Bio::Tools::Run::TigrAssembler, Bio::Factory::EMBOSS, Bio::Installer::EMBOSS, Bio::Tools::Run::EMBOSSApplication, Bio::Installer::Generic, Bio::Tools::Run::Phylo::QuickTree, Bio::Tools::Run::Alignment::Muscle, Bio::Tools::Run::Alignment::TCoffee, Bio::Tools::Run::Maq, Bio::Tools::Run::Alignment::Proda, Bio::Tools::Run::Alignment::Kalign, Bio::Tools::Run::Phylo::Hyphy::Modeltest, Bio::Tools::Run::Primer3, Bio::Tools::Run::Alignment::Exonerate, Bio::Tools::Run::Alignment::Pal2Nal, Bio::Tools::Run::Alignment::Amap, Bio::Tools::Run::Profile, Bio::Tools::Run::Phylo::Semphy, Bio::Tools::Run::Promoterwise, Bio::Tools::Run::Phylo::Phylip::Consense, Bio::Tools::Run::Alignment::MAFFT, Bio::Tools::Run::Alignment::Probalign, Bio::Tools::Run::Genscan, Bio::Tools::Run::Match, Bio::Tools::Run::Primate, Bio::Tools::Run::Phylo::Phylip::DrawTree, Bio::Tools::Run::Phylo::Phylip::ProtDist, Bio::Tools::Run::Phylo::PhyloBase, Bio::Installer::Clustalw, Bio::Tools::Run::Phylo::Phylip::PhylipConf, Bio::Tools::Run::Phylo::Phast::PhyloFit, Bio::Tools::Run::Simprot, Bio::Installer::PAML, Bio::Tools::Run::Analysis, Bio::Tools::Run::Alignment::DBA, Bio::DB::ESoap::WSDL, Bio::Installer::Probcons, Bio::Installer::SLR, Bio::Tools::Run::Phylo::Phylip::Base, Bio::Tools::Run::Phylo::Molphy::ProtML, Bio::Tools::Run::ERPIN, Bio::Tools::Run::Ensembl"
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   "file_build_pl" : "Build.PL",
   "file_changelog" : "Changes",
   "file_license" : "LICENSE",
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