Bio-VertRes-Config

Generate config files for the pathogen pipelines

Contents

• Introduction
• Installation
  • From Source
  • Running the tests
• Usage
• License
• Feedback/Issues

Introduction

Bio-VertRes-Config contains scripts for generating config files for the pathogen pipelines. It includes the following scripts:

• bacteria_register_and_qc_study - Register a bacteria study for import and QC with the Pathogen Informatics pipelines

• bacteria_mapping - Request the bacteria mapping pipeline to be run for a given dataset that is stored in the bacteria tracking database

• bacteria_snp_calling - Request the bacteria mapping and SNP calling pipeline to be run for a given dataset that is stored in the bacteria tracking database

• bacteria_assembly_and_annotation - Request the bacteria assembly and annotation pipeline to be run for a given dataset that is stored in the bacteria tracking database

• bacteria_rna_seq_expression - Request the RNA-seq expression analysis pipeline to be run for a given dataset that is stored in the bacteria tracking database

• bacteria_assembly_single_cell - Request the single cell assembly and annotation pipeline to be run for a given dataset

• bacteria_permissions - Create config scripts for pipeline permissions data

• eukaryote_register_and_qc_study - Register a eukaryote study for import and QC with the Pathogen Informatics pipelines

• eukaryote_mapping - Request the eukaryote mapping pipeline to be run for a given dataset that is stored in the eukaryote tracking database

• eukaryote_snp_calling - Request the eukaryote mapping and SNP calling pipeline to be run for a given dataset that is stored in the eukaryote tracking database

• eukaryote_assembly - Request the eukaryote assembly and annotation pipeline to be run for a given dataset that is stored in the eukaryote tracking database

• eukaryote_rna_seq_expression - Request the RNA-seq expression analysis pipeline to be run for a given dataset that is stored in the eukaryote tracking database

• helminth_register_and_qc_study - Register a helminth study for import and QC with the Pathogen Informatics pipelines

• helminth_mapping - Request the helminth mapping pipeline to be run for a given dataset that is stored in the helminth tracking database

• helminth_snp_calling - Request the helminth mapping and SNP calling pipeline to be run for a given dataset that is stored in the helminth tracking database

• helminth_rna_seq_expression - Request the RNA-seq expression analysis pipeline to be run for a given dataset that is stored in the helminth tracking database

• virus_register_and_qc_study - Register a virus study for import and QC with the Pathogen Informatics pipelines

• virus_mapping - Request the virus mapping pipeline to be run for a given dataset that is stored in the virus tracking database

• virus_snp_calling - Request the virus mapping and SNP calling pipeline to be run for a given dataset that is stored in the virus tracking database

• virus_assembly_and_annotation - Request the virus assembly and annotation pipeline to be run for a given dataset that is stored in the virus tracking database

• virus_rna_seq_expression - Request the RNA-seq expression analysis pipeline to be run for a given dataset that is stored in the virus tracking database

• pacbio_register - Register a pacbio study for import with the Pathogen Informatics pipelines

• setup_global_configs - Create config scripts and overall strucutre for the global configs

Installation

Details for installing Bio-VertRes-Config are provided below. If you encounter an issue when installing Bio-VertRes-Config please contact your local system administrator. If you encounter a bug please log it here or email us at [email protected].

From Source

Clone the repository:

git clone https://github.com/sanger-pathogens/Bio-VertRes-Config.git

Move into the directory and install all dependencies using DistZilla:

cd Bio-VertRes-Config
dzil authordeps --missing | cpanm
dzil listdeps --missing | cpanm

Run the tests:

dzil test
If the tests pass, install Bio-VertRes-Config:

dzil install

Running the tests

The tests can be run with dzil from the top level directory:

dzil test

Usage

Below is the usage for bacteria_register_and_qc_study. For usage options of the remaining scripts, run <script_name> --help.

Usage: bacteria_register_and_qc_study -t <ID type> -i <ID> -r <reference> [options]
Pipeline to register, QC, assemble and annotate a bacteria study.

Required:
  -t            STR Type (study/lane/file)
  -i            STR Study name, study ID, lane, file of lanes
  -r            STR Reference to QC against. Must match exactly one of the references from the -a option.

Options:
  -s            STR Limit to a single species name (e.g. 'Staphylococcus aureus')
  --assembler   STR Set a different assembler (spades/velvet/iva) [velvet]
  --spades_opts STR Modify parameters sent to SPAdes. Only --careful and --cov-cutoff auto are available. Default is none.
  --no_aa           Dont assemble or annotate
  -d            STR Specify a database [pathogen_prok_track]
  -c            STR Base directory to config files [/nfs/pathnfs05/conf]
  --root        STR Base directory for the pipelines [/lustre/scratch118/infgen/pathogen/pathpipe]
  --log         STR Base directory for the log files [/nfs/pathnfs05/log]
  --db_file     STR Filename containing database connection details [/software/pathogen/config/database_connection_details]
  -a            STR Search for available reference matching pattern and exit.
  -h                Print this message and exit

NOTE - If you are uncertain that your request was successful, please do NOT run the command again. Instead, please direct any queries to [email protected].

If you use the results of these pipelines, please acknowledge the pathogen informatics team and include the appropriate citations:

"Robust high throughput prokaryote de novo assembly and improvement pipeline for Illumina data"
Page AJ, De Silva, N., Hunt M, Quail MA, Parkhill J, Harris SR, Otto TD, Keane JA. (2016). Microbial Genomics 2(8) doi: 10.1099/mgen.0.000083

For more information on how to site the pipelines, please see:
http://mediawiki.internal.sanger.ac.uk/index.php/Pathogen_Informatics_Pipelines_-_Methods#Bacterial_Assembly_and_Annotation

For example usage and more information about the QC, assembly and annotation pipelines, please see:
http://mediawiki.internal.sanger.ac.uk/index.php/Pathogen_Informatics_Pipelines#QC_Pipeline
http://mediawiki.internal.sanger.ac.uk/index.php/Assembly_Pipeline_-_Pathogen_Informatics
http://mediawiki.internal.sanger.ac.uk/index.php/Pathogen_Informatics_Automated_Annotation_Pipeline

License

Bio-VertRes-Config is free software, licensed under GPLv3.

Feedback/Issues

Please report any issues to the issues page or email [email protected].