tweak_pipeline

SYNOPSIS

tweak_pipeline.pl [ -url mysql://user:pass@server:port/dbname | -reg_conf <reg_conf_file> -reg_alias <reg_alias> ] -tweak 'analysis[mafft%].analysis_capacity=undef'

DESCRIPTION

This is a script to “tweak” attributes or parameters of an existing eHive pipeline.

OPTIONS

--url <url>

URL defining where eHive database is located

--reg_conf <path>

path to a Registry configuration file

--reg_type <name>

Registry type of the eHive DBAdaptor

--reg_alias <name>

species/alias name for the eHive DBAdaptor

--nosqlvc

“No SQL Version Check” - set if you want to force working with a database created by a potentially schema-incompatible API

--tweak <string>

An assignment command that performs one individual “tweak”. You can “tweak” global/Analysis parameters, Analysis attributes and Resource Classes:

-tweak 'pipeline.param[take_time]=20'                   # override a value of a pipeline-wide parameter; can also create a non-existent parameter
-tweak 'analysis[take_b_apart].param[base]=10'          # override a value of an Analysis-wide parameter; can also create a non-existent parameter
-tweak 'analysis[add_together].analysis_capacity=undef' # override a value of an Analysis attribute
-tweak 'analysis[add_together].batch_size=15'           # override a value of an Analysis_stats attribute
-tweak 'analysis[part_multiply].resource_class=urgent'  # set the Resource Class of an Analysis (whether a Resource Class with this name existed or not)
-tweak 'resource_class[urgent].LSF=-q yesteryear'       # update or create a new Resource Description

If multiple “tweaks” are requested, they will be performed in the given order.

--DELETE <selector>

Shortcut to delete a parameter

--SHOW <selector>

Shortcut to show a parameter value