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Documentation

Create config scripts for assembly and annotation prokaryote data
Create config scripts for assembly and annotation prokaryote data
Create config scripts to map bacteria
Create config scripts for registering and QC of a prokaryote study
Create config scripts to map and run the rna seq expression pipeline
Create config scripts to map and snp call bacteria
Create config scripts for assembly and annotation prokaryote data
Create config scripts to map eukaryotes
Create config scripts for registering and QC of a eukaryotes study
Create config scripts to map and run the rna seq expression pipeline
Create config scripts to map and snp call eukaryotes
Create config scripts to map helminth
Create config scripts for registering and QC of a helminth study
Create config scripts to map and run the rna seq expression pipeline
Create config scripts to map and snp call helminth
Create config scripts and overall strucutre for the global configs
Create config scripts for assembly and annotation of a virus study
Create config scripts to map viruses
Create config scripts for registering and QC of a virus study
Create config scripts to map and run the rna seq expression pipeline
Create config scripts to map and snp call viruses

Modules

Create config files for the vr-codebase pipelines
Create config scripts to map bacteria
Create config scripts to map helminths
Create config scripts to map and run the rna seq expression pipeline
Create config scripts to map and snp call bacteria.
Create config scripts to map eukaryotes
Create config scripts to map and run the rna seq expression pipeline
Create config scripts to map and snp call bacteria.
Create config scripts to map helminths
Create config scripts to map helminths
Create config scripts to map and run the rna seq expression pipeline
Create config scripts to map and snp call bacteria.
A class to represent multiple top level files. It splits out mixed config files into the correct top level files
A role to handle references in a command line script
Prevent a study name from being registered in two different databases
Create config scripts to map viruses
Create config scripts to map helminths
Create config scripts to map and run the rna seq expression pipeline
Create config scripts to map and snp call bacteria.
Exceptions for input data
A class to represent multiple top level files. It splits out mixed config files into the correct top level files
A class for generating the AnnotateAssembly pipeline config file which annotates an assembly
A base class for generating the Assembly pipeline config file which archives data to nfs units
The base class for the bam improvement pipeline.
Base class for the BWA mapper
Base class for the BWA mapper
A set of attributes common to all pipeline config files
A class for generating the Import pipeline config file
The base class for the mapping pipeline.
A class for generating the QC pipeline config file. This is done on a per study basis ususally (and filtered by species).
The base class for the RNA seq expression and TraDis pipeline.
Moose Role to set the logfile name and config filename to include the reference
Moose Role for dealing with limits meta data filters
Moose Role for where you want different prefixes to allow you to run the same pipeline multiple times on the same data
Moose Role for translating non standard database names to their area
Base class for the smalt mapper
The base class for the SNP calling pipeline.
A base class for generating an Assembly pipeline config file using spades
Base class for the Ssaha2 mapper
Base class for the Stampy mapper
A class for generating the Store pipeline config file which archives data to nfs units
Base class for the Tophat mapper
Create TraDIS config files
A base class for generating an Assembly pipeline config file using velvet
Create the assembly and anntation files only, so no reference required, but for it to run you need to have done QC first
Create the assembly and anntation files only, so no reference required, but for it to run you need to have done QC first
Standard snp calling pipeline for bacteria
Standard snp calling pipeline for bacteria
Standard snp calling pipeline for bacteria
Standard snp calling pipeline for bacteria
Standard snp calling pipeline for bacteria
Standard snp calling pipeline for bacteria
Standard snp calling pipeline for bacteria
Standard snp calling pipeline for bacteria
Standard snp calling pipeline for bacteria
Standard snp calling pipeline for bacteria
Standard snp calling pipeline for bacteria
Standard snp calling pipeline for bacteria
Standard snp calling pipeline for bacteria
Standard snp calling pipeline for bacteria
Standard snp calling pipeline for bacteria
Standard snp calling pipeline for bacteria
Common base for recipes
Create the assemblyfiles only, so no reference required, but for it to run you need to have done QC first
Standard snp calling pipeline for bacteria
Standard snp calling pipeline for bacteria
Standard snp calling pipeline for bacteria
Standard snp calling pipeline for bacteria
Standard snp calling pipeline for bacteria
Standard snp calling pipeline for bacteria
Standard snp calling pipeline for bacteria
Standard snp calling pipeline for bacteria
Standard snp calling pipeline for eukaryotes
Standard snp calling pipeline for bacteria
Standard snp calling pipeline for bacteria
Standard snp calling pipeline for bacteria
Standard snp calling pipeline for bacteria
Standard snp calling pipeline for bacteria
Setting up global config files
Moose Role which creates the Euk mapping objects
Moose Role which creates the rna seq expression object
Moose Role which creates the bacteria snp calling object
Moose Role for creating all the global config files after creation
Moose Role which creates the Euk mapping objects
Moose Role which creates the rna seq expression object
Moose Role which creates the bacteria snp calling object
Attributes for working with references
Moose Role for registering a study
Moose Role which creates the Euk mapping objects
Moose Role which creates the rna seq expression object
Moose Role which creates the virus snp calling object
Create the assembly and anntation files only, so no reference required, but for it to run you need to have done QC first
Standard snp calling pipeline for virus
Standard snp calling pipeline for virus
Standard snp calling pipeline for virus
Standard snp calling pipeline for virus
Standard snp calling pipeline for virus
Standard snp calling pipeline for virus
Standard snp calling pipeline for virus
Standard snp calling pipeline for virus
Standard snp calling pipeline for virus
Standard snp calling pipeline for virus
Standard snp calling pipeline for virus
Standard snp calling pipeline for virus
Standard snp calling pipeline for virus
Standard snp calling pipeline for virus
Standard snp calling pipeline for virus
A class for translating between a reference name and the location on disk
A top level config file for a pipeline
Moose types to use for validation.
Check to see if a file exists. For validation when classes have input files.
Validates a prefix for use in filenames within the pipeline