TOC for all levels
ensembl-pipeline
ensembl-pipeline::java
ensembl-pipeline::java::pipeview
ensembl-pipeline::java::pipeview::jars
ensembl-pipeline::java::pipeview::src
ensembl-pipeline::java::pipeview::src::pathsteps
ensembl-pipeline::java::pipeview::src::pathsteps::common
ensembl-pipeline::java::pipeview::src::pathsteps::control
ensembl-pipeline::java::pipeview::src::pathsteps::gui
ensembl-pipeline::java::pipeview::src::pathsteps::gui::graph
ensembl-pipeline::java::pipeview::src::pathsteps::model
ensembl-pipeline::java::pipeview::src::pathsteps::test
ensembl-pipeline::modules
ensembl-pipeline::modules::Bio
ensembl-pipeline::modules::Bio::EnsEMBL
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Alignment
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::BatchSubmission
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Config
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Config::GeneBuild
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Config::Protein_Annotation
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Config::PseudoGenes
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Config::cDNAs_ESTs
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::DB
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::DBSQL
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::DBSQL::Finished
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::DBSQL::Protein
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Finished
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::GeneComparison
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::GeneDuplication
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::IDFactory
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Job
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Monitor
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Process
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Runnable
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Runnable::Protein
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::RunnableDB
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::RunnableDB::Protein
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::SeqFetcher
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::SubmissionSystem
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Task
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Task::RDB
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Task::RDB::Blast
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Task::Utils
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Tools
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Tools::BPlite
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Tools::Pmatch
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Transitions
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Utils
ensembl-pipeline::modules::t
ensembl-pipeline::modules::t::data
ensembl-pipeline::modules::t::data::ests
ensembl-pipeline::modules::t::dumps
ensembl-pipeline::modules::t::pipeline
ensembl-pipeline::modules::t::sptr
ensembl-pipeline::scripts
ensembl-pipeline::scripts::Pre-release-site
ensembl-pipeline::scripts::Pseudogenes
ensembl-pipeline::scripts::Sequence
ensembl-pipeline::scripts::cDNA_update
ensembl-pipeline::scripts::chr_subseq
ensembl-pipeline::scripts::compara
ensembl-pipeline::scripts::mRNA
ensembl-pipeline::scripts::ncRNA
ensembl-pipeline::scripts::post_GeneBuild
ensembl-pipeline::scripts::protein_pipeline
ensembl-pipeline::scripts::sql
ensembl-pipeline::scripts::wga2genes
ensembl-pipeline::scripts::AlignWise
ensembl-pipeline::scripts::DataConversion
ensembl-pipeline::scripts::DataConversion::flybase
ensembl-pipeline::scripts::DataConversion::medaka
ensembl-pipeline::scripts::DataConversion::mitochondria
ensembl-pipeline::scripts::DataConversion::tetraodon
ensembl-pipeline::scripts::DataConversion::tetraodon::annotation
ensembl-pipeline::scripts::DataConversion::tetraodon::assembly
ensembl-pipeline::scripts::DataConversion::wormbase
ensembl-pipeline::scripts::EST
ensembl-pipeline::scripts::EST::dust
ensembl-pipeline::scripts::Features
ensembl-pipeline::scripts::Finished
ensembl-pipeline::scripts::Finished::assembly
ensembl-pipeline::scripts::Finished::assembly::AssemblyMapper
ensembl-pipeline::scripts::GeneBuild
ensembl-pipeline::scripts::GeneComparison
ensembl-pipeline::scripts::HMMs
ensembl-pipeline::scripts::LowCoverage
ensembl-pipeline::scripts::LowCoverage::generic_config
ensembl-pipeline::scripts::LowCoverage::generic_config::Bio
ensembl-pipeline::scripts::LowCoverage::generic_config::Bio::EnsEMBL
ensembl-pipeline::scripts::LowCoverage::generic_config::Bio::EnsEMBL::Analysis
ensembl-pipeline::scripts::LowCoverage::generic_config::Bio::EnsEMBL::Analysis::Config
ensembl-pipeline::scripts::LowCoverage::generic_config::Bio::EnsEMBL::Pipeline
ensembl-pipeline::scripts::LowCoverage::generic_config::Bio::EnsEMBL::Pipeline::Config
ensembl-pipeline::scripts::LowCoverage::generic_config::Bio::EnsEMBL::Pipeline::Config::GeneBuild
ensembl-pipeline::scripts::LowCoverage::generic_config::Bio::EnsEMBL::Pipeline::Config::Protein_Annotation
ensembl-pipeline::scripts::LowCoverage::generic_config::Bio::EnsEMBL::Pipeline::Config::PseudoGenes
ensembl-pipeline::scripts::LowCoverage::generic_config::Bio::EnsEMBL::Pipeline::Config::cDNAs_ESTs
ensembl-pipeline::scripts::LowCoverage::generic_config::pipe_conf
ensembl-pipeline::scripts::ModelTraining
ensembl-pipeline::sql
ensembl-pipeline::test_system
ensembl-pipeline::test_system::config
ensembl-pipeline::test_system::config::Bio
ensembl-pipeline::test_system::config::Bio::EnsEMBL
ensembl-pipeline::test_system::config::Bio::EnsEMBL::Analysis
ensembl-pipeline::test_system::config::Bio::EnsEMBL::Analysis::Config
ensembl-pipeline::test_system::config::Bio::EnsEMBL::Analysis::Config::GeneBuild
ensembl-pipeline::test_system::config::Bio::EnsEMBL::Pipeline
ensembl-pipeline::test_system::config::Bio::EnsEMBL::Pipeline::Config
ensembl-pipeline::test_system::config::Bio::EnsEMBL::Pipeline::Config::GeneBuild
ensembl-pipeline::test_system::config::Bio::EnsEMBL::Pipeline::Config::Protein_Annotation
ensembl-pipeline::test_system::config::Bio::EnsEMBL::Pipeline::Config::PseudoGenes
ensembl-pipeline::test_system::config::Bio::EnsEMBL::Pipeline::Config::cDNAs_ESTs
ensembl-pipeline::test_system::docs
ensembl-pipeline::test_system::modules
ensembl-pipeline::test_system::reference_data
ensembl-pipeline::test_system::setup
ensembl-pipelineTop
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ensembl-pipeline::javaTop
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ensembl-pipeline::java::pipeviewTop
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ensembl-pipeline::java::pipeview::jarsTop
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ensembl-pipeline::java::pipeview::srcTop
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ensembl-pipeline::java::pipeview::src::pathstepsTop
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ensembl-pipeline::java::pipeview::src::pathsteps::commonTop
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ensembl-pipeline::java::pipeview::src::pathsteps::controlTop
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ensembl-pipeline::java::pipeview::src::pathsteps::guiTop
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ensembl-pipeline::java::pipeview::src::pathsteps::gui::graphTop
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ensembl-pipeline::java::pipeview::src::pathsteps::modelTop
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ensembl-pipeline::java::pipeview::src::pathsteps::testTop
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ensembl-pipeline::modulesTop
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ensembl-pipeline::modules::BioTop
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ensembl-pipeline::modules::Bio::EnsEMBLTop
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ensembl-pipeline::modules::Bio::EnsEMBL::PipelineTop
AlignmentBio::EnsEMBL::Pipeline::Alignment.pm
AnaSubmission
Analysis
BatchSubmissionBio::EnsEMBL::Pipeline::BatchSubmission
FlagBio::EnsEMBL::Pipeline::Flag
Job(1)Bio::EnsEMBL::Pipeline::Job
Monitor
RuleBio::EnsEMBL::Pipeline::Rule
RuleManager(1)Bio::EnsEMBL::Pipeline::RuleManager
SeqFetcherBio::EnsEMBL::Pipeline::SeqFetcher
Statussmall object storing job status tags
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::AlignmentTop
AlignmentSeqBio::EnsEMBL::Pipeline::Alignment::AlignmentSeq.pm
AlignmentSquizz
AlignmentStatsBio::EnsEMBL::Pipeline::Alignment::AlignmentStats
EvidenceAlignmentBio::EnsEMBL::Pipeline::Alignment::EvidenceAlignment
InformativeSites
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::BatchSubmissionTop
Dummy
GridEngineBio::EnsEMBL::Pipeline::BatchSubmission::GridEngine
LSFBio::EnsEMBL::Pipeline::BatchSubmission::LSF
Local
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::ConfigTop
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ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Config::GeneBuildTop
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ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Config::Protein_AnnotationTop
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ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Config::PseudoGenesTop
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ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Config::cDNAs_ESTsTop
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ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::DBTop
Nothing here
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::DBSQLTop
AnalysisAdaptorBio::EnsEMBL::DBSQL::Pipeline::AnalysisAdaptor
CompressedDnaAlignFeatureAdaptorAdaptor for compressed DnaAlignFeatures
DBAdaptor(1)adapter class for EnsEMBL Pipeline DB
FlagAdaptorBio::EnsEMBL::Pipeline::DBSQL::FlagAdaptor
JobAdaptor(1)Bio::EnsEMBL::Pipeline::DBSQL::JobAdaptor
RuleAdaptorBio::EnsEMBL::Pipeline::DBSQL::RuleAdaptor
StateInfoContainer(1)Bio::EnsEMBL::Pipeline::DBSQL::StateInfoContainer
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::DBSQL::FinishedTop
DBAdaptor(2)Bio::EnsEMBL::Pipeline::DBSQL::Finished::DBAdaptor
DnaAlignFeatureAdaptor
HitDescriptionAdaptor
JobAdaptor(2)Bio::EnsEMBL::Pipeline::DBSQL::Finished::JobAdaptor
ProteinAlignFeatureAdaptor
StateInfoContainer(2)Bio::EnsEMBL::Pipeline::DBSQL::Finished::StateinfoContainer
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::DBSQL::ProteinTop
Nothing here
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::FinishedTop
HitDescription
Job(2)Bio::EnsEMBL::Pipeline::Finished::Job
RuleManager(2)Bio::EnsEMBL::Pipeline::Finished::RuleManager.pm
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::GeneComparisonTop
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ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::GeneDuplicationTop
CodonBasedAlignmentBio::EnsEMBL::Pipeline::GeneDuplication::CodonBasedAlignment
Finder
PAML
Result
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::IDFactoryTop
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ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::JobTop
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ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::MonitorTop
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ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::ProcessTop
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ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::RunnableTop
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ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Runnable::ProteinTop
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ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::RunnableDBTop
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ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::RunnableDB::ProteinTop
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ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::SeqFetcherTop
BPIndexBio::EnsEMBL::Pipeline::SeqFetcher::BPIndex
BioIndexBio::EnsEMBL::Pipeline::SeqFetcher::BioIndex
DBIndex
EfetchBio::EnsEMBL::Pipeline::SeqFetcher::Efetch
FetchFromBlastDB
FileIndexBio::EnsEMBL::Pipeline::SeqFetcher::Pfetch
Finished_Dfetch
Finished_Pfetch
GetseqsBio::EnsEMBL::Pipeline::SeqFetcher::Getseqs
GetzBio::EnsEMBL::Pipeline::SeqFetcher::Getz
MfetchBio::EnsEMBL::Pipeline::SeqFetcher::Mfetch
OBDAIndexSeqFetcherBio::EnsEMBL::Pipeline::SeqFetcher::OBDAIndexSeqFetcher
PfetchBio::EnsEMBL::Pipeline::SeqFetcher::Pfetch
xdgetBio::EnsEMBL::Pipeline::SeqFetcher::xdget
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::SubmissionSystemTop
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ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::TaskTop
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ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Task::RDBTop
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ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Task::RDB::BlastTop
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ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Task::UtilsTop
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ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::ToolsTop
Embl
MM_Taxonomy
ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Tools::BPliteTop
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ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::Tools::PmatchTop
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ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::TransitionsTop
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ensembl-pipeline::modules::Bio::EnsEMBL::Pipeline::UtilsTop
InputIDFactory
PipelineSanityChecks
SliceDump
ensembl-pipeline::modules::tTop
EnsTestDB
ensembl-pipeline::modules::t::dataTop
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ensembl-pipeline::modules::t::data::estsTop
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ensembl-pipeline::modules::t::dumpsTop
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ensembl-pipeline::modules::t::pipelineTop
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ensembl-pipeline::modules::t::sptrTop
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ensembl-pipeline::scriptsTop
AnalysisCreationAnalysisCreation
Node
RuleCreationRuleCreation
ensembl-pipeline::scripts::Pre-release-siteTop
Nothing here
ensembl-pipeline::scripts::PseudogenesTop
Nothing here
ensembl-pipeline::scripts::SequenceTop
Nothing here
ensembl-pipeline::scripts::cDNA_updateTop
cDNAUpdatecDNAupdate.pm
ensembl-pipeline::scripts::chr_subseqTop
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ensembl-pipeline::scripts::comparaTop
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ensembl-pipeline::scripts::mRNATop
Nothing here
ensembl-pipeline::scripts::ncRNATop
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ensembl-pipeline::scripts::post_GeneBuildTop
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ensembl-pipeline::scripts::protein_pipelineTop
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ensembl-pipeline::scripts::sqlTop
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ensembl-pipeline::scripts::wga2genesTop
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ensembl-pipeline::scripts::AlignWiseTop
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ensembl-pipeline::scripts::DataConversionTop
Nothing here
ensembl-pipeline::scripts::DataConversion::flybaseTop
FlyBaseGff
FlyBaseToolbox
ensembl-pipeline::scripts::DataConversion::medakaTop
MedakaConf
ensembl-pipeline::scripts::DataConversion::mitochondriaTop
MitConf
ensembl-pipeline::scripts::DataConversion::tetraodonTop
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ensembl-pipeline::scripts::DataConversion::tetraodon::annotationTop
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ensembl-pipeline::scripts::DataConversion::tetraodon::assemblyTop
Nothing here
ensembl-pipeline::scripts::DataConversion::wormbaseTop
Clone2Acc
WormBaseWormBase
ensembl-pipeline::scripts::ESTTop
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ensembl-pipeline::scripts::EST::dustTop
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ensembl-pipeline::scripts::FeaturesTop
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ensembl-pipeline::scripts::FinishedTop
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ensembl-pipeline::scripts::Finished::assemblyTop
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ensembl-pipeline::scripts::Finished::assembly::AssemblyMapperTop
BlastzAlignermodule to do a whole genome alignment between two closely related assemblies and create assembly entries from it.
ensembl-pipeline::scripts::GeneBuildTop
SimilarityInputIdConfig
ensembl-pipeline::scripts::GeneComparisonTop
Nothing here
ensembl-pipeline::scripts::HMMsTop
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ensembl-pipeline::scripts::LowCoverageTop
LowCoverageGeneBuildConf
ensembl-pipeline::scripts::LowCoverage::generic_configTop
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ensembl-pipeline::scripts::LowCoverage::generic_config::BioTop
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ensembl-pipeline::scripts::LowCoverage::generic_config::Bio::EnsEMBLTop
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ensembl-pipeline::scripts::LowCoverage::generic_config::Bio::EnsEMBL::AnalysisTop
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ensembl-pipeline::scripts::LowCoverage::generic_config::Bio::EnsEMBL::Analysis::ConfigTop
Blast(1)Bio::EnsEMBL::Analysis::Config::Blast
General(1)Bio::EnsEMBL::Analysis::Config::General
ensembl-pipeline::scripts::LowCoverage::generic_config::Bio::EnsEMBL::PipelineTop
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ensembl-pipeline::scripts::LowCoverage::generic_config::Bio::EnsEMBL::Pipeline::ConfigTop
BatchQueue(1)Bio::EnsEMBL::Pipeline::Config::BatchQueue
General(2)Bio::EnsEMBL::Pipeline::Config::General
ensembl-pipeline::scripts::LowCoverage::generic_config::Bio::EnsEMBL::Pipeline::Config::GeneBuildTop
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ensembl-pipeline::scripts::LowCoverage::generic_config::Bio::EnsEMBL::Pipeline::Config::Protein_AnnotationTop
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ensembl-pipeline::scripts::LowCoverage::generic_config::Bio::EnsEMBL::Pipeline::Config::PseudoGenesTop
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ensembl-pipeline::scripts::LowCoverage::generic_config::Bio::EnsEMBL::Pipeline::Config::cDNAs_ESTsTop
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ensembl-pipeline::scripts::LowCoverage::generic_config::pipe_confTop
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ensembl-pipeline::scripts::ModelTrainingTop
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ensembl-pipeline::sqlTop
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ensembl-pipeline::test_systemTop
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ensembl-pipeline::test_system::configTop
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ensembl-pipeline::test_system::config::BioTop
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ensembl-pipeline::test_system::config::Bio::EnsEMBLTop
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ensembl-pipeline::test_system::config::Bio::EnsEMBL::AnalysisTop
Nothing here
ensembl-pipeline::test_system::config::Bio::EnsEMBL::Analysis::ConfigTop
Blast(2)Bio::EnsEMBL::Analysis::Config::Blast
Databases Bio::EnsEMBL::Analysis::Config::Databases
General(3)Bio::EnsEMBL::Analysis::Config::General
ensembl-pipeline::test_system::config::Bio::EnsEMBL::Analysis::Config::GeneBuildTop
Pmatch
ensembl-pipeline::test_system::config::Bio::EnsEMBL::PipelineTop
Nothing here
ensembl-pipeline::test_system::config::Bio::EnsEMBL::Pipeline::ConfigTop
BatchQueue(2)Bio::EnsEMBL::Pipeline::Config::BatchQueue
General(4)Bio::EnsEMBL::Pipeline::Config::General
ensembl-pipeline::test_system::config::Bio::EnsEMBL::Pipeline::Config::GeneBuildTop
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ensembl-pipeline::test_system::config::Bio::EnsEMBL::Pipeline::Config::Protein_AnnotationTop
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ensembl-pipeline::test_system::config::Bio::EnsEMBL::Pipeline::Config::PseudoGenesTop
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ensembl-pipeline::test_system::config::Bio::EnsEMBL::Pipeline::Config::cDNAs_ESTsTop
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ensembl-pipeline::test_system::docsTop
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ensembl-pipeline::test_system::modulesTop
Environment
FeatureComparison
RunTest
TestDB
ensembl-pipeline::test_system::reference_dataTop
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ensembl-pipeline::test_system::setupTop