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 |