diff --git a/scripts/beekeeper.pl b/scripts/beekeeper.pl
index d4d57e0283c64a45a454a65327e29e05a6cc4ecf..9ebe2d06fa8e6482a453b760138a57c7c1cdce1a 100755
--- a/scripts/beekeeper.pl
+++ b/scripts/beekeeper.pl
@@ -24,14 +24,6 @@ sub main {
# the globals into a nice '$self' package
my $self = {};
- $self->{'db_conf'} = {
- -host => '',
- -port => 3306,
- -user => 'ensro',
- -pass => '',
- -dbname => '',
- };
-
my $help;
my $loopit = 0;
my $sync = 0;
@@ -69,11 +61,6 @@ sub main {
'reg_conf|regfile=s' => \$self->{'reg_conf'},
'reg_alias|regname=s'=> \$self->{'reg_alias'},
'url=s' => \$self->{'url'},
- 'host|dbhost=s' => \$self->{'db_conf'}->{'-host'},
- 'port|dbport=i' => \$self->{'db_conf'}->{'-port'},
- 'user|dbuser=s' => \$self->{'db_conf'}->{'-user'},
- 'password|dbpass=s' => \$self->{'db_conf'}->{'-pass'},
- 'database|dbname=s' => \$self->{'db_conf'}->{'-dbname'},
# loop control
'run' => \$run,
@@ -115,9 +102,6 @@ sub main {
'reset_all|reset_all_jobs_for_analysis=s' => \$reset_all_jobs_for_analysis,
'job_output=i' => \$job_id_for_output,
'monitor!' => \$self->{'monitor'},
-
- # loose arguments interpreted as database name (for compatibility with mysql[dump])
- '<>', sub { $self->{'db_conf'}->{'-dbname'} = shift @_; },
);
if ($help) { script_usage(0); }
@@ -140,12 +124,8 @@ sub main {
$self->{'dba'} = Bio::EnsEMBL::Registry->get_DBAdaptor($self->{'reg_alias'}, 'hive');
} elsif($self->{'url'}) {
$self->{'dba'} = Bio::EnsEMBL::Hive::URLFactory->fetch($self->{'url'}) || die("Unable to connect to $self->{'url'}\n");
- } elsif ( $self->{'db_conf'}->{'-host'}
- and $self->{'db_conf'}->{'-user'}
- and $self->{'db_conf'}->{'-dbname'}) { # connect to database specified
- $self->{'dba'} = Bio::EnsEMBL::Hive::DBSQL::DBAdaptor->new( %{$self->{'db_conf'}} );
} else {
- print "\nERROR : Connection parameters (reg_conf+reg_alias, url or dbhost+dbuser+dbname) need to be specified\n\n";
+ print "\nERROR : Connection parameters (url or reg_conf+reg_alias) need to be specified\n\n";
script_usage(1);
}
@@ -404,9 +384,6 @@ __DATA__
=head1 USAGE EXAMPLES
# Usually run after the pipeline has been created to calculate the internal statistics necessary for eHive functioning
- beekeeper.pl --host=hostname --port=3306 --user=username --password=secret ehive_dbname -sync
-
- # An alternative way of doing the same thing
beekeeper.pl -url mysql://username:secret@hostname:port/ehive_dbname -sync
# Do not run any additional Workers, just check for the current status of the pipeline:
@@ -434,11 +411,6 @@ __DATA__
-reg_conf <path> : path to a Registry configuration file
-reg_alias <string> : species/alias name for the Hive DBAdaptor
-url <url string> : url defining where hive database is located
- -host <machine> : mysql database host <machine>
- -port <port#> : mysql port number
- -user <name> : mysql connection user <name>
- -password <pass> : mysql connection password <pass>
- [-database] <name> : mysql database <name>
=head2 Looping control
diff --git a/scripts/init_pipeline.pl b/scripts/init_pipeline.pl
index 4470a050edfb48a8203f40d9b34f14fb756dc345..5014f5255c4c9ded55e5f543a8e50424431e3640 100755
--- a/scripts/init_pipeline.pl
+++ b/scripts/init_pipeline.pl
@@ -33,7 +33,7 @@ __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> [-help | [-analysis_topup | -job_topup] <options_for_this_particular_pipeline>]
=head1 DESCRIPTION
diff --git a/scripts/runWorker.pl b/scripts/runWorker.pl
index 7b6aac6d17fb02b881b86c39c631e3abf99161a3..c12e0ff212a607c00b64cde1fc4b567ed43e73e5 100755
--- a/scripts/runWorker.pl
+++ b/scripts/runWorker.pl
@@ -11,14 +11,6 @@ use Bio::EnsEMBL::Hive::Valley;
Bio::EnsEMBL::Registry->no_version_check(1);
-my $db_conf = {
- -host => '',
- -port => 3306,
- -user => 'ensro',
- -pass => '',
- -dbname => '',
-};
-
my ($reg_conf, $reg_alias, $url); # Connection parameters
my ($resource_class_id, $resource_class_name, $analysis_id, $logic_name, $job_id); # Task specification parameters
my ($job_limit, $life_span, $no_cleanup, $no_write, $hive_log_dir, $worker_log_dir, $retry_throwing_jobs, $compile_module_once, $force); # Worker control parameters
@@ -30,11 +22,6 @@ GetOptions(
'reg_conf|regfile=s' => \$reg_conf,
'reg_alias|regname=s' => \$reg_alias,
'url=s' => \$url,
- 'host|dbhost=s' => \$db_conf->{'-host'},
- 'port|dbport=i' => \$db_conf->{'-port'},
- 'user|dbuser=s' => \$db_conf->{'-user'},
- 'password|dbpass=s' => \$db_conf->{'-pass'},
- 'database|dbname=s' => \$db_conf->{'-dbname'},
# Task specification parameters:
'rc_id=i' => \$resource_class_id,
@@ -57,9 +44,6 @@ GetOptions(
# Other commands
'h|help' => \$help,
'debug=i' => \$debug,
-
-# loose arguments interpreted as database name (for compatibility with mysql[dump])
- '<>', sub { $db_conf->{'-dbname'} = shift @_; },
);
if ($help) { script_usage(0); }
@@ -83,24 +67,20 @@ if($reg_alias) {
$url =~ s/\$((\w+))/defined($ENV{$2})?"$ENV{$2}":"\$$1"/eg;
$DBA = Bio::EnsEMBL::Hive::URLFactory->fetch($url) or die "Unable to connect to '$url'\n";
-} elsif ($db_conf->{'-host'} and $db_conf->{'-user'} and $db_conf->{'-dbname'}) {
- $DBA = Bio::EnsEMBL::Hive::DBSQL::DBAdaptor->new( %$db_conf );
} else {
- print "\nERROR : Connection parameters (reg_conf+reg_alias, url or dbhost+dbuser+dbname) need to be specified\n\n";
+ print "\nERROR : Connection parameters (url or reg_conf+reg_alias) need to be specified\n\n";
script_usage(1);
}
unless($DBA and $DBA->isa("Bio::EnsEMBL::Hive::DBSQL::DBAdaptor")) {
- print "ERROR : no database connection\n\n";
- script_usage(1);
+ print "ERROR : no database connection\n\n";
+ script_usage(1);
}
my $queen = $DBA->get_Queen();
my ($meadow_type, $meadow_name, $process_id, $exec_host) = Bio::EnsEMBL::Hive::Valley->new()->whereami();
-print "runWorker(-MeadowType => $meadow_type, -MeadowName => $meadow_name, -ProcessId => $process_id, -ExecHost => $exec_host)\n";
-
my $worker;
eval {
@@ -169,30 +149,24 @@ __DATA__
=head1 USAGE EXAMPLES
# Run one local worker process in ehive_dbname and let the system pick up the analysis
- runWorker.pl --host=hostname --port=3306 --user=username --password=secret ehive_dbname
-
- # Run one local worker process in ehive_dbname and let the system pick up the analysis (another connection syntax)
runWorker.pl -url mysql://username:secret@hostname:port/ehive_dbname
+ # Run one local worker process in ehive_dbname and let the system pick up the analysis from the given resource_class
+ runWorker.pl -url mysql://username:secret@hostname:port/ehive_dbname -rc_name low_mem
+
# Run one local worker process in ehive_dbname and specify the logic_name
runWorker.pl -url mysql://username:secret@hostname:port/ehive_dbname -logic_name fast_blast
- # Run a specific job (by a local worker process):
+ # Run a specific job in a local worker process:
runWorker.pl -url mysql://username:secret@hostname:port/ehive_dbname -job_id 123456
=head1 OPTIONS
=head2 Connection parameters:
- -conf <path> : config file describing db connection
-reg_conf <path> : path to a Registry configuration file
-reg_alias <string> : species/alias name for the Hive DBAdaptor
-url <url string> : url defining where database is located
- -host <machine> : mysql database host <machine>
- -port <port#> : mysql port number
- -user <name> : mysql connection user <name>
- -password <pass> : mysql connection password
- [-database] <name> : mysql database <name>
=head2 Task specificaton parameters:
@@ -212,7 +186,7 @@ __DATA__
-worker_log_dir <path> : directory where stdout/stderr of this particular worker is redirected
-retry_throwing_jobs <0|1> : if a job dies *knowingly*, should we retry it by default?
-compile_module_once 0|1 : should we compile the module only once (desired future behaviour), or pretend to do it before every job (current behaviour)?
- -force 0|1 : set to 1 if you want to force running a Worker over a BLOCKED analysis
+ -force 0|1 : set to 1 if you want to force running a Worker over a BLOCKED analysis or to run a specific DONE/SEMAPHORED job_id
=head2 Other options: