Andrew Page > Bio-VertRes-Config-1.133090

Bio-VertRes-Config-1.133090

This Release Bio-VertRes-Config-1.133090  [Download] [Browse 05 Nov 2013
Links Discussion Forum ] [ View/Report Bugs ] [ Website ] [ Dependencies ] [ Other Tools ]
Repository https://github.com/sanger-pathogens/Bio-VertRes-Config.git
CPAN Testers PASS (50)   FAIL (274)   NA (7)   UNKNOWN (2)   [ View Reports ] [ Perl/Platform Version Matrix ]
Rating      (0 Reviews) [ Rate this distribution ]
License The GNU General Public License, Version not specified
Special Files
LICENSE
Makefile.PL
MANIFEST
META.yml
README

Modules

Bio::VertRes::Config Create config files for the vr-codebase pipelines      
Bio::VertRes::Config::CommandLine::BacteriaAssemblyAndAnnotation Create assembly and annotation files      
Bio::VertRes::Config::CommandLine::BacteriaAssemblySingleCell Create assembly and annotation files      
Bio::VertRes::Config::CommandLine::BacteriaMapping Create config scripts to map bacteria      
Bio::VertRes::Config::CommandLine::BacteriaRegisterAndQCStudy Create config scripts to map helminths      
Bio::VertRes::Config::CommandLine::BacteriaRnaSeqExpression Create config scripts to map and run the rna seq expression pipeline      
Bio::VertRes::Config::CommandLine::BacteriaSnpCalling Create config scripts to map and snp call bacteria.      
Bio::VertRes::Config::CommandLine::Common Create config scripts      
Bio::VertRes::Config::CommandLine::ConstructLimits Put the limits together      
Bio::VertRes::Config::CommandLine::EukaryotesAssembly Create assembly files      
Bio::VertRes::Config::CommandLine::EukaryotesMapping Create config scripts to map eukaryotes      
Bio::VertRes::Config::CommandLine::EukaryotesRegisterAndQCStudy Create config scripts to map helminths      
Bio::VertRes::Config::CommandLine::EukaryotesRnaSeqExpression Create config scripts to map and run the rna seq expression pipeline      
Bio::VertRes::Config::CommandLine::EukaryotesSnpCalling Create config scripts to map and snp call bacteria.      
Bio::VertRes::Config::CommandLine::HelminthMapping Create config scripts to map helminths      
Bio::VertRes::Config::CommandLine::HelminthRegisterAndQCStudy Create config scripts to map helminths      
Bio::VertRes::Config::CommandLine::HelminthRnaSeqExpression Create config scripts to map and run the rna seq expression pipeline      
Bio::VertRes::Config::CommandLine::HelminthSnpCalling Create config scripts to map and snp call bacteria.      
Bio::VertRes::Config::CommandLine::LogParameters A class to represent multiple top level files. It splits out mixed config files into the correct top level files      
Bio::VertRes::Config::CommandLine::ReferenceHandlingRole A role to handle references in a command line script      
Bio::VertRes::Config::CommandLine::StudyNameSearch Prevent a study name from being registered in two different databases      
Bio::VertRes::Config::CommandLine::VirusAssemblyAndAnnotation Create assembly and annotation files      
Bio::VertRes::Config::CommandLine::VirusMapping Create config scripts to map viruses      
Bio::VertRes::Config::CommandLine::VirusRegisterAndQCStudy Create config scripts to map helminths      
Bio::VertRes::Config::CommandLine::VirusRnaSeqExpression Create config scripts to map and run the rna seq expression pipeline      
Bio::VertRes::Config::CommandLine::VirusSnpCalling Create config scripts to map and snp call bacteria.      
Bio::VertRes::Config::Exceptions Exceptions for input data      
Bio::VertRes::Config::MultipleTopLevelFiles A class to represent multiple top level files. It splits out mixed config files into the correct top level files      
Bio::VertRes::Config::Pipelines::AnnotateAssembly A class for generating the AnnotateAssembly pipeline config file which annotates an assembly      
Bio::VertRes::Config::Pipelines::Assembly A base class for generating the Assembly pipeline config file which archives data to nfs units      
Bio::VertRes::Config::Pipelines::BamImprovement The base class for the bam improvement pipeline.      
Bio::VertRes::Config::Pipelines::Bowtie2Mapping Base class for the BWA mapper      
Bio::VertRes::Config::Pipelines::BwaMapping Base class for the BWA mapper      
Bio::VertRes::Config::Pipelines::Common A set of attributes common to all pipeline config files      
Bio::VertRes::Config::Pipelines::Import A class for generating the Import pipeline config file      
Bio::VertRes::Config::Pipelines::Mapping The base class for the mapping pipeline.      
Bio::VertRes::Config::Pipelines::QC A class for generating the QC pipeline config file. This is done on a per study basis ususally (and filtered by species).      
Bio::VertRes::Config::Pipelines::RnaSeqExpression The base class for the RNA seq expression and TraDis pipeline.      
Bio::VertRes::Config::Pipelines::Roles::FilenameWithReference Moose Role to set the logfile name and config filename to include the reference      
Bio::VertRes::Config::Pipelines::Roles::MetaDataFilter Moose Role for dealing with limits meta data filters      
Bio::VertRes::Config::Pipelines::Roles::MultiplePrefix Moose Role for where you want different prefixes to allow you to run the same pipeline multiple times on the same data      
Bio::VertRes::Config::Pipelines::Roles::RootDatabaseLookup Moose Role for translating non standard database names to their area      
Bio::VertRes::Config::Pipelines::SmaltMapping Base class for the smalt mapper      
Bio::VertRes::Config::Pipelines::SnpCalling The base class for the SNP calling pipeline.      
Bio::VertRes::Config::Pipelines::SpadesAssembly A base class for generating an Assembly pipeline config file using spades      
Bio::VertRes::Config::Pipelines::Ssaha2Mapping Base class for the Ssaha2 mapper      
Bio::VertRes::Config::Pipelines::StampyMapping Base class for the Stampy mapper      
Bio::VertRes::Config::Pipelines::Store A class for generating the Store pipeline config file which archives data to nfs units      
Bio::VertRes::Config::Pipelines::TophatMapping Base class for the Tophat mapper      
Bio::VertRes::Config::Pipelines::Tradis Create TraDIS config files      
Bio::VertRes::Config::Pipelines::VelvetAssembly A base class for generating an Assembly pipeline config file using velvet      
Bio::VertRes::Config::Recipes::BacteriaAssemblyAndAnnotation Create the assembly and anntation files only, so no reference required, but for it to run you need to have done QC first      
Bio::VertRes::Config::Recipes::BacteriaAssemblySingleCell Create the assembly and anntation files only, so no reference required, but for it to run you need to have done QC first      
Bio::VertRes::Config::Recipes::BacteriaMappingUsingBowtie2 Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::BacteriaMappingUsingBwa Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::BacteriaMappingUsingSmalt Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::BacteriaMappingUsingSsaha2 Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::BacteriaMappingUsingStampy Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::BacteriaMappingUsingTophat Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::BacteriaRegisterAndQCStudy Register and QC a study      
Bio::VertRes::Config::Recipes::BacteriaRnaSeqExpressionUsingBowtie2 Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::BacteriaRnaSeqExpressionUsingBwa Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::BacteriaRnaSeqExpressionUsingSmalt Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::BacteriaRnaSeqExpressionUsingStampy Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::BacteriaRnaSeqExpressionUsingTophat Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::BacteriaSnpCallingUsingBowtie2 Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::BacteriaSnpCallingUsingBwa Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::BacteriaSnpCallingUsingSmalt Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::BacteriaSnpCallingUsingSsaha2 Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::BacteriaSnpCallingUsingStampy Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::Common Common base for recipes      
Bio::VertRes::Config::Recipes::EukaryotesAssembly Create the assemblyfiles only, so no reference required, but for it to run you need to have done QC first      
Bio::VertRes::Config::Recipes::EukaryotesMappingUsingBowtie2 Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::EukaryotesMappingUsingBwa Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::EukaryotesMappingUsingSmalt Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::EukaryotesMappingUsingSsaha2 Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::EukaryotesMappingUsingStampy Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::EukaryotesMappingUsingTophat Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::EukaryotesRegisterAndQCStudy Register and QC a study      
Bio::VertRes::Config::Recipes::EukaryotesRnaSeqExpressionUsingBowtie2 Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::EukaryotesRnaSeqExpressionUsingBwa Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::EukaryotesRnaSeqExpressionUsingSmalt Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::EukaryotesRnaSeqExpressionUsingStampy Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::EukaryotesRnaSeqExpressionUsingTophat Standard snp calling pipeline for eukaryotes      
Bio::VertRes::Config::Recipes::EukaryotesSnpCallingUsingBowtie2 Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::EukaryotesSnpCallingUsingBwa Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::EukaryotesSnpCallingUsingSmalt Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::EukaryotesSnpCallingUsingSsaha2 Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::EukaryotesSnpCallingUsingStampy Standard snp calling pipeline for bacteria      
Bio::VertRes::Config::Recipes::Global Setting up global config files      
Bio::VertRes::Config::Recipes::HelminthRegisterAndQCStudy Register and QC a study      
Bio::VertRes::Config::Recipes::Roles::BacteriaMapping Moose Role which creates the Euk mapping objects      
Bio::VertRes::Config::Recipes::Roles::BacteriaRegisterStudy Moose Role for registering a study      
Bio::VertRes::Config::Recipes::Roles::BacteriaRnaSeqExpression Moose Role which creates the rna seq expression object      
Bio::VertRes::Config::Recipes::Roles::BacteriaSnpCalling Moose Role which creates the bacteria snp calling object      
Bio::VertRes::Config::Recipes::Roles::CreateGlobal Moose Role for creating all the global config files after creation      
Bio::VertRes::Config::Recipes::Roles::EukaryotesMapping Moose Role which creates the Euk mapping objects      
Bio::VertRes::Config::Recipes::Roles::EukaryotesRegisterStudy Moose Role for registering a study      
Bio::VertRes::Config::Recipes::Roles::EukaryotesRnaSeqExpression Moose Role which creates the rna seq expression object      
Bio::VertRes::Config::Recipes::Roles::EukaryotesSnpCalling Moose Role which creates the bacteria snp calling object      
Bio::VertRes::Config::Recipes::Roles::Reference Attributes for working with references      
Bio::VertRes::Config::Recipes::Roles::RegisterStudy Moose Role for registering a study      
Bio::VertRes::Config::Recipes::Roles::VirusMapping Moose Role which creates the Euk mapping objects      
Bio::VertRes::Config::Recipes::Roles::VirusRegisterStudy Moose Role for registering a study      
Bio::VertRes::Config::Recipes::Roles::VirusRnaSeqExpression Moose Role which creates the rna seq expression object      
Bio::VertRes::Config::Recipes::Roles::VirusSnpCalling Moose Role which creates the virus snp calling object      
Bio::VertRes::Config::Recipes::VirusAssemblyAndAnnotation Create the assembly and anntation files only, so no reference required, but for it to run you need to have done QC first      
Bio::VertRes::Config::Recipes::VirusMappingUsingBowtie2 Standard snp calling pipeline for virus      
Bio::VertRes::Config::Recipes::VirusMappingUsingBwa Standard snp calling pipeline for virus      
Bio::VertRes::Config::Recipes::VirusMappingUsingSmalt Standard snp calling pipeline for virus      
Bio::VertRes::Config::Recipes::VirusMappingUsingSsaha2 Standard snp calling pipeline for virus      
Bio::VertRes::Config::Recipes::VirusMappingUsingStampy Standard snp calling pipeline for virus      
Bio::VertRes::Config::Recipes::VirusMappingUsingTophat Standard snp calling pipeline for virus      
Bio::VertRes::Config::Recipes::VirusRegisterAndQCStudy Register and QC a study      
Bio::VertRes::Config::Recipes::VirusRnaSeqExpressionUsingBowtie2 Standard snp calling pipeline for virus      
Bio::VertRes::Config::Recipes::VirusRnaSeqExpressionUsingBwa Standard snp calling pipeline for virus      
Bio::VertRes::Config::Recipes::VirusRnaSeqExpressionUsingSmalt Standard snp calling pipeline for virus      
Bio::VertRes::Config::Recipes::VirusRnaSeqExpressionUsingStampy Standard snp calling pipeline for virus      
Bio::VertRes::Config::Recipes::VirusRnaSeqExpressionUsingTophat Standard snp calling pipeline for virus      
Bio::VertRes::Config::Recipes::VirusSnpCallingUsingBowtie2 Standard snp calling pipeline for virus      
Bio::VertRes::Config::Recipes::VirusSnpCallingUsingBwa Standard snp calling pipeline for virus      
Bio::VertRes::Config::Recipes::VirusSnpCallingUsingSmalt Standard snp calling pipeline for virus      
Bio::VertRes::Config::Recipes::VirusSnpCallingUsingSsaha2 Standard snp calling pipeline for virus      
Bio::VertRes::Config::Recipes::VirusSnpCallingUsingStampy Standard snp calling pipeline for virus      
Bio::VertRes::Config::References A class for translating between a reference name and the location on disk      
Bio::VertRes::Config::RegisterStudy Register a study      
Bio::VertRes::Config::TopLevel A top level config file for a pipeline      
Bio::VertRes::Config::Types Moose types to use for validation.      
Bio::VertRes::Config::Validate::File Check to see if a file exists. For validation when classes have input files.      
Bio::VertRes::Config::Validate::Prefix Validates a prefix for use in filenames within the pipeline      

Documentation

bacteria_assembly_and_annotation Create config scripts for assembly and annotation prokaryote data  
bacteria_mapping Create config scripts to map bacteria  
bacteria_rna_seq_expression Create config scripts to map and run the rna seq expression pipeline  
bacteria_snp_calling Create config scripts to map and snp call bacteria  
eukaryote_assembly Create config scripts for assembly and annotation prokaryote data  
eukaryote_mapping Create config scripts to map eukaryotes  
eukaryote_rna_seq_expression Create config scripts to map and run the rna seq expression pipeline  
eukaryote_snp_calling Create config scripts to map and snp call eukaryotes  
helminth_mapping Create config scripts to map helminth  
helminth_rna_seq_expression Create config scripts to map and run the rna seq expression pipeline  
helminth_snp_calling Create config scripts to map and snp call helminth  
register_and_qc_study Create config scripts for registering and QC of a virus study  
setup_global_configs Create config scripts and overall strucutre for the global configs  
virus_assembly_and_annotation Create config scripts for assembly and annotation of a virus study  
virus_mapping Create config scripts to map viruses  
virus_rna_seq_expression Create config scripts to map and run the rna seq expression pipeline  
virus_snp_calling Create config scripts to map and snp call viruses  

Other Files

README.md