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

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

parent 54cee0e3
......@@ -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');
sub main {
my %deprecated_option = ();
GetOptions( \%deprecated_option,
'analysis_topup!', # always on
'job_topup!', # never, use
if($deprecated_option{'job_topup'}) {
die "-job_topup mode has been discontinued. Please use instead.\n";
if($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 $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();
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