Bio-Path-Find

A tool for finding information about pathogen sequencing runs.

Contents

• Introduction
• Installation
  • Required dependencies
  • From Source
  • Running the tests
• Usage
• License
• Feedback/Issues
• Further Information

Introduction

These scripts can be used for accessing the results of the pathogen informatics analysis pipelines.

Installation

Bio-Path-find has the following dependencies:

Required dependencies

• Bio-Metagenomics
• Bio-Track-Schema
• Bio-Sequencescape-Schema

Details for installing Bio-Path-Find are provided below. If you encounter an issue when installing Bio-Path-Find 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-Path-Find.git

Move into the directory and install all dependencies using DistZilla:

cd Bio-Path-Find
dzil authordeps --missing | cpanm
dzil listdeps --missing | cpanm

Run the tests:

dzil test
If the tests pass, install Bio-Path-Find:

dzil install

Running the tests

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

dzil test

Usage

usage:
      pf <command> --id <ID or file> --type <ID type> [options]

description:
    The pathfind commands find and display various kinds of information about
    sequencing projects.

    Run "pf man" to see full documentation for this main "pf" command. Run "pf
    man <command>" or "pf <command> --help" to see documentation for a
    particular sub-command.

global options:
    --csv-separator -c          field separator to use when writing CSV files
                                [Default:","; Env: PF_CSV_SEP]
    --file-id-type --ft         type of IDs in the input file [Default:"lane"
                                ; Possible values: lane, library, sample,
                                species, study]
    --force -F                  force commands to overwrite existing files [
                                Flag; Env: PF_FORCE_OVERWRITE]
    --help -h --usage -?        Prints this usage information. [Flag]
    --id -i                     ID or name of file containing IDs [Required;
                                Env: PF_ID]
    --ignore-processed-flag -I  ignore "processed" flag when finding lanes [
                                Flag]
    --no-progress-bars -N       don't show progress bars [Flag; Env: PF_NO_
                                PROGRESS_BARS]
    --rename -r                 replace hash (#) with underscore (_) in
                                filenames [Flag]
    --type -t                   ID type. Use "file" to read IDs from file [
                                Required; Possible values: database, file,
                                lane, library, sample, species, study; Env:
                                PF_TYPE]
    --verbose -v                show debugging messages [Default:"0"; Integer
                                ; Env: PF_VERBOSE]

available commands:
    accession        Find accessions for sequencing runs
    annotation       Find annotation results
    assembly         Find genome assemblies
    bash_completion  Bash completion automator
    data             Find files and directories
    help             Prints this usage information
    info             Find information about samples
    man              Full manpage
    map              Find mapped bam files for lanes
    qc               Find quality control information about samples
    ref              Find reference genomes
    rnaseq           Find RNA-Seq results
    snp              Find VCF files for lanes
    status           Find the status of samples
    supplementary    Get supplementary information about samples

License

Bio-Path-Find is free software, licensed under GPLv3.

Feedback/Issues

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

Further Information

Sanger Institute staff should refer to the wiki for further information.