changed name to more intuitive run.pl

misc-scripts/id_mapping/run_all.pl

-#!/usr/local/bin/perl
-
-=head1 NAME
-
-run_all.pl - wrapper script to run the stable ID mapping
-
-=head1 SYNOPSIS
-
-run_all.pl [arguments]
-
-Required arguments:
-
-  --dbname, db_name=NAME              database name NAME
-  --host, --dbhost, --db_host=HOST    database host HOST
-  --port, --dbport, --db_port=PORT    database port PORT
-  --user, --dbuser, --db_user=USER    database username USER
-  --pass, --dbpass, --db_pass=PASS    database passwort PASS
-
-Optional arguments:
-
-  --conffile, --conf=FILE             read parameters from FILE
-                                      (default: conf/Conversion.ini)
-
-  --logfile, --log=FILE               log to FILE (default: *STDOUT)
-  --logpath=PATH                      write logfile to PATH (default: .)
-  --logappend, --log_append           append to logfile (default: truncate)
-  --loglevel=LEVEL                    define log level (default: INFO)
-
-  -i, --interactive=0|1               run script interactively (default: true)
-  -n, --dry_run, --dry=0|1            don't write results to database
-  -h, --help, -?                      print help (this message)
-
-=head1 DESCRIPTION
-
-
-=head1 LICENCE
-
-This code is distributed under an Apache style licence. Please see
-http://www.ensembl.org/info/about/code_licence.html for details.
-
-=head1 AUTHOR
-
-Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team
-
-=head1 CONTACT
-
-Please post comments/questions to the Ensembl development list
-<ensembl-dev@ebi.ac.uk>
-
-=cut
-
-use strict;
-use warnings;
-no warnings 'uninitialized';
-
-use FindBin qw($Bin);
-use Bio::EnsEMBL::Utils::ConfParser;
-use Bio::EnsEMBL::Utils::Logger;
-
-# parse configuration and commandline arguments
-my $conf = new Bio::EnsEMBL::Utils::ConfParser(
-  -SERVERROOT => "$Bin/../../..",
-  -DEFAULT_CONF => "$Bin/default.conf"
-);
-
-$conf->parse_options(
-  'sourcehost|source_host=s' => 1,
-  'sourceport|source_port=n' => 1,
-  'sourceuser|source_user=s' => 1,
-  'sourcepass|source_pass=s' => 0,
-  'sourcedbname|source_dbname=s' => 1,
-  'targethost|target_host=s' => 1,
-  'targetport|target_port=n' => 1,
-  'targetuser|target_user=s' => 1,
-  'targetpass|target_pass=s' => 0,
-  'targetdbname|target_dbname=s' => 1,
-  'mode=s' => 0,
-  'dumppath|dump_path=s' => 1,
-  'chromosomes|chr=s@' => 0,
-  'region=s' => 0,
-  'biotypes=s@' => 0,
-  'min_exon_length|minexonlength=i' => 0,
-  'exonerate_path|exoneratepath=s' => 1,
-  'exonerate_threshold|exoneratethreshold=f' => 0,
-  'exonerate_jobs|exoneratejobs=i' => 0,
-  'exonerate_bytes_per_job|exoneratebytesperjob=f' => 0,
-);
-
-# get log filehandle and print heading and parameters to logfile
-my $logger = new Bio::EnsEMBL::Utils::Logger(
-  -LOGFILE    => $conf->param('logfile'),
-  -LOGPATH    => $conf->param('logpath'),
-  -LOGAPPEND  => $conf->param('logappend'),
-  -LOGLEVEL     => $conf->param('loglevel'),
-);
-
-# initialise log
-$logger->init_log($conf->list_param_values);
-
-# this script is only a wrapper and will run one or more components.
-# define options for the components here.
-my %options;
-
-$options{'dump_cache'} = $conf->create_commandline_options(
-  interactive => 0,
-  is_component => 1,
-);
-
-$options{'id_mapping'} = $conf->create_commandline_options(
-  interactive => 0,
-  is_component => 1,
-);
-
-# run components, depending on mode
-my $mode = $conf->param('mode') || 'normal';
-my $sub = "run_$mode";
-no strict 'refs';
-&$sub;
-
-# finish logfile
-$logger->finish_log;
-
-### END main ###
-
-
-sub run_normal {
-  
-  # dump cache files (this is done for all modes)
-  &run_component('dump_cache.pl', $options{'dump_cache'}, 'building cache');
-
-  # ID mapping
-  &run_component('id_mapping.pl', $options{'id_mapping'}, 'Id mapping');
-
-  # archive
-  #&run_component('archive.pl', $options{'archive'}, 'archive');
-
-  # reporting
-  #&run_component('report.pl', $options{'report'}, 'creating report');
-
-  # QC
-  #&run_component('qc.pl', $options{'qc'}, 'QC');
-
-}
-
-
-sub run_component {
-  my $cmd = shift;
-  my $options = shift;
-  my $logtext = shift || $cmd;
-
-  $logger->info("----- $logtext -----\n", 0, 'stamped');
-
-  system("./$cmd $options") == 0
-    or $logger->error("Error running $cmd. Please see the respective logfile for more information.\n");
-  
-  $logger->info("----- done with $logtext -----\n\n", 0, 'stamped');
-}
-