Commit 6e8b91eb authored by Leo Gordon's avatar Leo Gordon
Browse files

cosmetic: removed mention of no-longer-used options -analysis_topup and -job_topup from the docs

parent a28ef353
#!/usr/bin/env perl
# A generic loader of hive pipelines.
#
# Because all of the functionality is hidden in Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf
# you can create pipelines by calling the right methods of HiveGeneric_conf directly,
# so this script is just a commandline wrapper that can conveniently find modules by their filename.
# A generic script for creating Hive pipelines from PipeConfig module files (see below for docs)
use strict;
use warnings;
......@@ -67,7 +63,7 @@ __DATA__
=head1 SYNOPSIS
init_pipeline.pl <config_module_or_filename> [-help | [-analysis_topup | -job_topup] <options_for_this_particular_pipeline>]
init_pipeline.pl <config_module_or_filename> [<options_for_this_particular_pipeline>]
=head1 DESCRIPTION
......@@ -81,23 +77,12 @@ __DATA__
# initialize a generic eHive pipeline:
init_pipeline.pl Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf -password <yourpassword>
# see what command line options are available when initializing long multiplication example pipeline
# (assuming your current directory is ensembl-hive/modules/Bio/EnsEMBL/Hive) :
init_pipeline.pl PipeConfig/LongMult_conf -help
# initialize the long multiplicaton pipeline by supplying not only mandatory but also optional data:
# (assuming your current directory is ensembl-hive/modules/Bio/EnsEMBL/Hive/PipeConfig) :
init_pipeline.pl LongMult_conf -password <yourpassword> -first_mult 375857335 -second_mult 1111333355556666
=head1 OPTIONS
-help : Gets this help message and exits
-analysis_topup : A special initialization mode when (1) pipeline_create_commands are switched off and (2) only newly defined analyses are added to the database
This mode is only useful in the process of putting together a new pipeline.
-job_topup : Another special initialization mode when only jobs are created - no other structural changes to the pipeline are acted upon.
-hive_force_init : If set to 1, forces the (re)creation of the hive database even if a previous version of it is present in the server.
=head1 LICENSE
......
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