Setup a vrtracking pipeline
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.
setup_tracking has the following dependencies:
The test can be run with dzil from the top level directory:
dzil test
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.
setup_tracking is free software, licensed under GPLv3.
Please report any issues to the issues page or email path-help@sanger.ac.uk.