diff --git a/misc-scripts/id_mapping/default.conf b/misc-scripts/id_mapping/default.conf
new file mode 100644
index 0000000000000000000000000000000000000000..f3a3e09a08d9e18e4328910c389f60bcc4d1b593
--- /dev/null
+++ b/misc-scripts/id_mapping/default.conf
@@ -0,0 +1,26 @@
+; for dry runs, no data is written to the database
+dry_run = 1
+
+; verbose logging
+verbose = 1
+
+; prepend this path to your 'log' parameter
+logpath = /ecs2/work2/pm2/logs/test
+
+; old db settings
+oldhost = ecs4
+oldport = 3350
+olduser = ensro
+olddbname = pm2_homo_sapiens_core_39_36a
+
+; new db settings
+newhost = ecs4
+newport = 3350
+newuser = ensadmin
+newpass = ensembl
+newdbname = pm2_homo_sapiens_core_39_36a
+
+; cache
+dumppath = /ecs2/scratch3/pm2/data/test
+;region = chromosome:NCBI36:X:1000000:2000000:1
+
diff --git a/misc-scripts/id_mapping/dump_cache.pl b/misc-scripts/id_mapping/dump_cache.pl
new file mode 100755
index 0000000000000000000000000000000000000000..fbadd1cf50bdf023a86bb9ba957344df3704bbdd
--- /dev/null
+++ b/misc-scripts/id_mapping/dump_cache.pl
@@ -0,0 +1,153 @@
+#!/usr/local/bin/perl
+
+=head1 NAME
+
+
+=head1 SYNOPSIS
+
+.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)
+
+ -v, --verbose=0|1 verbose logging (default: false)
+ -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($Bin);
+use vars qw($SERVERROOT);
+
+BEGIN {
+ $SERVERROOT = "$Bin/../../..";
+ unshift(@INC, "$SERVERROOT/ensembl/modules");
+ unshift(@INC, "$SERVERROOT/bioperl-live");
+}
+
+use Getopt::Long;
+use Pod::Usage;
+use Bio::EnsEMBL::Utils::ConfParser;
+use Bio::EnsEMBL::Utils::Logger;
+use Bio::EnsEMBL::IdMapping::Cache;
+
+$| = 1;
+
+my $conf = new Bio::EnsEMBL::Utils::ConfParser(
+ -SERVERROOT => $SERVERROOT,
+);
+
+# parse options
+$conf->param('default_conf', './default.conf');
+$conf->parse_common_options(@_);
+$conf->parse_extra_options(qw(
+ oldhost|old_host=s
+ oldport|old_port=n
+ olduser|old_user=s
+ oldpass|old_pass=s
+ olddbname|old_dbname=s
+ newhost|new_host=s
+ newport|new_port=n
+ newuser|new_user=s
+ newpass|new_pass=s
+ newdbname|new_dbname=s
+ dumppath|dump_path=s
+ cachefile|cache_file=s
+ chromosomes|chr=s@
+ region=s
+ biotypes=s@
+));
+$conf->allowed_params(
+ $conf->get_common_params,
+ qw(
+ oldhost oldport olduser oldpass olddbname
+ newhost newport newuser newpass newdbname
+ dumppath cachefile
+ chromosomes region biotypes
+ )
+);
+
+if ($conf->param('help') or $conf->error) {
+ warn $conf->error if $conf->error;
+ pod2usage(1);
+}
+
+# ask user to confirm parameters to proceed
+$conf->confirm_params;
+
+# 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'),
+ -VERBOSE => $conf->param('verbose'),
+ -IS_COMPONENT => $conf->param('is_component'),
+);
+
+# initialise log
+$logger->init_log($conf->list_all_params);
+
+# check required parameters were set
+$conf->check_required_params(
+ qw(
+ oldhost oldport olduser olddbname
+ newhost newport newuser newdbname
+ dumppath
+ )
+);
+
+my $cache = new Bio::EnsEMBL::IdMapping::Cache(
+ -LOGGER => $logger,
+ -CONF => $conf,
+);
+
+unless ($cache->cache_file_exists) {
+ # load objects from database
+ $cache->build_cache;
+
+ # write cache to file
+ $cache->write_to_file;
+}
+
+# finish logfile
+$logger->finish_log;
+
+
+### END main ###
+
diff --git a/misc-scripts/id_mapping/run_all.pl b/misc-scripts/id_mapping/run_all.pl
new file mode 100755
index 0000000000000000000000000000000000000000..7b748d1a3eb2b8947d577f7931ed8c158123941a
--- /dev/null
+++ b/misc-scripts/id_mapping/run_all.pl
@@ -0,0 +1,176 @@
+#!/usr/local/bin/perl
+
+=head1 NAME
+
+
+=head1 SYNOPSIS
+
+.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)
+
+ -v, --verbose=0|1 verbose logging (default: false)
+ -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($Bin);
+use vars qw($SERVERROOT);
+
+BEGIN {
+ $SERVERROOT = "$Bin/../../..";
+ unshift(@INC, "$SERVERROOT/ensembl/modules");
+ unshift(@INC, "$SERVERROOT/bioperl-live");
+}
+
+use Getopt::Long;
+use Pod::Usage;
+use Bio::EnsEMBL::Utils::ConfParser;
+use Bio::EnsEMBL::Utils::Logger;
+
+$| = 1;
+
+my $conf = new Bio::EnsEMBL::Utils::ConfParser(
+ -SERVERROOT => $SERVERROOT,
+);
+
+# parse options
+$conf->param('default_conf', './default.conf');
+$conf->parse_common_options(@_);
+$conf->parse_extra_options(qw(
+ oldhost|old_host=s
+ oldport|old_port=n
+ olduser|old_user=s
+ oldpass|old_pass=s
+ olddbname|old_dbname=s
+ newhost|new_host=s
+ newport|new_port=n
+ newuser|new_user=s
+ newpass|new_pass=s
+ newdbname|new_dbname=s
+ dumppath|dump_path=s
+ cachefile|cache_file=s
+ chromosomes|chr=s@
+ region=s
+ biotypes=s@
+));
+$conf->allowed_params(
+ $conf->get_common_params,
+ qw(
+ oldhost oldport olduser oldpass olddbname
+ newhost newport newuser newpass newdbname
+ dumppath cachefile
+ chromosomes region biotypes
+ )
+);
+
+if ($conf->param('help') or $conf->error) {
+ warn $conf->error if $conf->error;
+ pod2usage(1);
+}
+
+# ask user to confirm parameters to proceed
+$conf->confirm_params;
+
+# 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'),
+ -VERBOSE => $conf->param('verbose'),
+);
+
+# initialise log
+$logger->init_log($conf->list_all_params);
+
+# check required parameters were set
+$conf->check_required_params(
+ qw(
+ oldhost oldport olduser olddbname
+ newhost newport newuser newdbname
+ dumppath
+ )
+);
+
+# create commandline options for running component scripts
+my $options = $conf->create_commandline_options(
+ -ALLOWED_PARAMS => 1,
+ -REPLACE => {
+ interactive => 0,
+ is_component => 1,
+ },
+);
+
+# dump cache files
+&run_component('dump_cache.pl', $options, 'building cache');
+
+# ID mapping
+#&run_component('id_mapping.pl', $options, 'Id mapping');
+
+# archive
+#&run_component('archive.pl', $options, 'archive');
+
+# reporting
+#&run_component('report.pl', $options, 'creating report');
+
+# QC
+#&run_component('qc.pl', $options, 'QC');
+
+
+# finish logfile
+$logger->finish_log;
+
+
+### END main ###
+
+sub run_component {
+ my $cmd = shift;
+ my $options = shift;
+ my $logtext = shift || $cmd;
+
+ $logger->log_stamped("----- $logtext -----\n");
+
+ system("./$cmd $options") == 0
+ or $logger->log_error("Error running $cmd. Please see the respective logfile for more information.\n");
+
+ $logger->log_stamped("----- done with $logtext -----\n\n");
+}
+