setup_tracking's Introduction

setup_tracking

Setup a vrtracking pipeline

Introduction
Installation
- Required dependencies
- Running the tests
Usage
License
Feedback/Issues

Introduction

setup_tracking is used to set up a new vrtrack pipeline. It creates a database and initally seeds it. It creates directories and config files and outputs a line to add to the crontab.

Installation

setup_tracking has the following dependencies:

Required dependencies

vr-codebase

Running the tests

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

dzil test

Usage

setup_tracking.pl -h

Usage: ./bin/setup_tracking.pl [options] short_name
  -d|pipeline_base_directory  <Base directory for pipeline defaults to /lustre/scratch118/infgen/pathogen/pathpipe>
  -c|config_base_directory    <Config file directory, defaults to /nfs/pathnfs01/conf>
  -l|log_base_directory       <Log file directory, defaults to /nfs/pathnfs01/log>
  -p|prefix                   <prefix of database name, defaults to pathogen>
  -s|suffix                   <suffix of database name, defaults to external>
  -e|environment              <production or test, defaults to production>
  -n|no_populate_assembly     <do not populate assembly table>
  -h|help                     <print this message>

Defaults should be find for pathogens, so typical usage is:
./bin/setup_tracking.pl abc
which creates a database called pathogen_abc_external,
config files in /nfs/pathnfs01/conf/pathogen_abc_external
and pipeline files in /lustre/scratch118/infgen/pathogen/pathpipe/pathogen_abc_external/seq-pipelines

Setup a new vrtrack pipeline. It creates a database, initally seeds it, creates directories, creates config files and outputs the line to add to the crontab.