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