Commit 48e960ae authored by Leo Gordon's avatar Leo Gordon
Browse files

removed references to old config file as obsolete

parent 805aca4c
......@@ -32,7 +32,7 @@ sub main {
-dbname => '',
};
my ($help, $conf_file);
my $help;
my $loopit = 0;
my $sync = 0;
my $local = 0;
......@@ -65,7 +65,6 @@ sub main {
GetOptions(
# connection parameters
'conf=s' => \$conf_file,
'reg_conf|regfile=s' => \$self->{'reg_conf'},
'reg_alias|regname=s'=> \$self->{'reg_alias'},
'url=s' => \$self->{'url'},
......@@ -121,8 +120,6 @@ sub main {
if ($help) { script_usage(0); }
parse_conf($self, $conf_file);
if($run or $run_job_id) {
$max_loops = 1;
} elsif ($loopit or $keep_alive) {
......@@ -272,23 +269,6 @@ sub main {
#######################
sub parse_conf {
my ($self, $conf_file) = @_;
if($conf_file and (-e $conf_file)) {
#read configuration file from disk
my @conf_list = @{do $conf_file};
foreach my $confPtr (@conf_list) {
#print("HANDLE type " . $confPtr->{TYPE} . "\n");
if(($confPtr->{TYPE} eq 'COMPARA') or ($confPtr->{TYPE} eq 'DATABASE')) {
$self->{'db_conf'} = $confPtr;
}
}
}
}
# --------------[worker reports]--------------------
sub show_given_workers {
......
......@@ -19,7 +19,7 @@ my $db_conf = {
-dbname => '',
};
my ($conf_file, $reg_conf, $reg_alias, $url); # Connection parameters
my ($reg_conf, $reg_alias, $url); # Connection parameters
my ($rc_id, $logic_name, $analysis_id, $input_id, $job_id); # Task specification parameters
my ($job_limit, $life_span, $no_cleanup, $no_write, $hive_output_dir, $worker_output_dir, $retry_throwing_jobs); # Worker control parameters
my ($help, $debug, $show_analysis_stats);
......@@ -27,7 +27,6 @@ my ($help, $debug, $show_analysis_stats);
GetOptions(
# Connection parameters:
'conf=s' => \$conf_file,
'reg_conf|regfile=s' => \$reg_conf,
'reg_alias|regname=s' => \$reg_alias,
'url=s' => \$url,
......@@ -64,8 +63,6 @@ GetOptions(
if ($help) { script_usage(0); }
parse_conf($conf_file);
if($reg_conf) { # if reg_conf is defined, we load it regardless of whether it is used to connect to the Hive database or not:
Bio::EnsEMBL::Registry->load_all($reg_conf);
}
......@@ -146,28 +143,6 @@ if($show_analysis_stats) {
exit 0;
#######################
#
# subroutines
#
#######################
sub parse_conf {
my $conf_file = shift;
if($conf_file and (-e $conf_file)) {
#read configuration file from disk
my @conf_list = @{do $conf_file};
foreach my $confPtr (@conf_list) {
#print("HANDLE type " . $confPtr->{TYPE} . "\n");
if(($confPtr->{TYPE} eq 'COMPARA') or ($confPtr->{TYPE} eq 'DATABASE')) {
$db_conf = $confPtr;
}
}
}
}
__DATA__
......
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