Commit 6dd08829 authored by Leo Gordon's avatar Leo Gordon
Browse files

incompatible_change: -analysis_topup always on, -job_topup dropped in fav. of seed_pipeline.pl

parent 54cee0e3
...@@ -18,16 +18,31 @@ BEGIN { ...@@ -18,16 +18,31 @@ BEGIN {
} }
use Getopt::Long qw(:config pass_through no_auto_abbrev);
use Bio::EnsEMBL::Hive::Utils ('script_usage', 'load_file_or_module'); use Bio::EnsEMBL::Hive::Utils ('script_usage', 'load_file_or_module');
sub main { sub main {
my %deprecated_option = ();
GetOptions( \%deprecated_option,
'analysis_topup!', # always on
'job_topup!', # never, use seed_pipeline.pl
);
if($deprecated_option{'job_topup'}) {
die "-job_topup mode has been discontinued. Please use seed_pipeline.pl instead.\n";
}
if($deprecated_option{'analysis_topup'}) {
die "-analysis_topup has been deprecated. Please note this script now *always* runs in -analysis_topup mode.\n";
}
my $file_or_module = shift @ARGV or script_usage(0); my $file_or_module = shift @ARGV or script_usage(0);
my $config_module = load_file_or_module( $file_or_module ); my $pipeconfig_package_name = load_file_or_module( $file_or_module );
my $config_object = $config_module->new(); my $pipeconfig_object = $pipeconfig_package_name->new();
$config_object->process_options(); $pipeconfig_object->process_options();
$config_object->run(); $pipeconfig_object->run();
$pipeconfig_object->show_useful_commands();
} }
main(); main();
......
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