seed_pipeline

SYNOPSIS

seed_pipeline.pl {-url <url> | -reg_conf <reg_conf> [-reg_type <reg_type>] -reg_alias <reg_alias>} [ {-analyses_pattern <pattern> | -analysis_id <analysis_id> | -logic_name <logic_name>} [ -input_id <input_id> ] ]

DESCRIPTION

seed_pipeline.pl is a generic script that is used to create {initial or top-up} Jobs for eHive pipelines

USAGE EXAMPLES

    # find out which analyses may need seeding (with an example input_id):

seed_pipeline.pl -url "mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/lg4_long_mult"

    # seed one Job into the "start" Analysis:

seed_pipeline.pl -url "mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/lg4_long_mult" \
                 -logic_name start -input_id '{"a_multiplier" => 2222222222, "b_multiplier" => 3434343434}'

OPTIONS

Connection parameters

--reg_conf <path>: path to a Registry configuration file
--reg_type <string>: type of the registry entry (“hive”, “core”, “compara”, etc - defaults to “hive”)
--reg_alias <string>: species/alias name for the eHive DBAdaptor
--url <url string>: URL defining where eHive database is located
--nosqlvc: “No SQL Version Check” - set if you want to force working with a database created by a potentially schema-incompatible API

Analysis parameters

--analyses_pattern <string>: seed Job(s) for analyses whose logic_name matches the supplied pattern
--analysis_id <num>: seed Job for Analysis with the given analysis_id

Input

--input_id <string>: specify the Job’s input parameters as a stringified hash
--semaphored: wrap the Job into a funnel Semaphore (provide a stable_id for the whole execution stream)

Other commands/options

-h, --help: show this help message