Raw content of Bio::EnsEMBL::Pipeline::Config::General
<![CDATA[# EnsEMBL module for Bio::EnsEMBL::Pipeline::Config::General;
#
# You may distribute this module under the same terms as perl itself
=head1 NAME
Bio::EnsEMBL::Pipeline::Config::General
=head1 SYNOPSIS
use Bio::EnsEMBL::Pipeline::Config::General;
use Bio::EnsEMBL::Pipeline::Config::General qw();
=head1 DESCRIPTION
General pipeline configuration.
It imports and sets a number of standard global variables into the
calling package. Without arguments all the standard variables are set,
and with a list, only those variables whose names are provided are set.
The module will die if a variable which doesn\'t appear in its
C<%Config> hash is asked to be set.
The variables can also be references to arrays or hashes.
Edit C<%Config> to add or alter variables.
All the variables are in capitals, so that they resemble environment
variables.
=head1 CONTACT
B<ensembl-dev@ebi.ac.uk>
=cut
package Bio::EnsEMBL::Pipeline::Config::General;
use strict;
use vars qw(%Config);
%Config = (
# binaries, libraries and data files
BIN_DIR => '/usr/local/ensembl/bin',
DATA_DIR => '/usr/local/ensembl/data',
LIB_DIR => '/usr/local/ensembl/lib',
# temporary working space (e.g. /tmp)
PIPELINE_WORK_DIR => '',
# default input_file_directory
PIPELINE_INPUT_DIR => '',
# default target_file_directory
PIPELINE_TARGET_DIR => '',
#regex for spiting up slice input_ids
SLICE_INPUT_ID_REGEX => '(\S+)\.(\d+)-(\d+):?([^:]*)',
PIPELINE_REPEAT_MASKING => ['RepeatMask'],
SNAP_MASKING => [],
MAX_JOB_TIME => 86400, # the max number of seconds a job should be
#spending in CPU time in LSF before being killed 86400 is 24 hours
KILLED_INPUT_IDS => '', # a path to produse a file of killed
# input_ids, good to have it local to the machine you running
# rulemanager on to prevent nfs stress
RENAME_ON_RETRY => 1, # toggle to see if you want the stdout/err
#files renamed when a job is retried
);
sub import {
my ($callpack) = caller(0); # Name of the calling package
my $pack = shift; # Need to move package off @_
# Get list of variables supplied, or else all
my @vars = @_ ? @_ : keys(%Config);
return unless @vars;
# Predeclare global variables in calling package
eval "package $callpack; use vars qw("
. join(' ', map { '$'.$_ } @vars) . ")";
die $@ if $@;
foreach (@vars) {
if (defined $Config{ $_ }) {
no strict 'refs';
# Exporter does a similar job to the following
# statement, but for function names, not
# scalar variables:
*{"${callpack}::$_"} = \$Config{ $_ };
} else {
die "Error: Config: $_ not known\n";
}
}
}
1;
]]>