diff --git a/misc-scripts/schema_patch.pl b/misc-scripts/schema_patch.pl
deleted file mode 100755
index 74859eb946982f8d5fc6e5c47dbcc3774834009b..0000000000000000000000000000000000000000
--- a/misc-scripts/schema_patch.pl
+++ /dev/null
@@ -1,234 +0,0 @@
-#!/usr/local/ensembl/bin/perl -w
-
-=head1 NAME
-
-schema_patch.pl - automagically apply schema patches to Ensembl dbs
-
-=head1 SYNOPSIS
-
-schema_patch.pl [arguments]
-
-Required arguments:
-
- --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
-
- --pattern, --dbpattern=PATTERN patch databases where name matches PATTERN
- Note that this is a database pattern of
- the form %core_41% rather than a regexp
- --schema, --dbschema=NUM patch to schema version NUM
- --schema_type Schema type to patch e.g. core|variation|funcgen
-
-Optional arguments:
-
- --conffile, --conf=FILE read parameters from FILE
- (default: conf/Conversion.ini)
-
- --bindir=DIR mysql binary directory (default:
- /usr/local/ensembl/bin)
-
- --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, --dry_run=0|1 don't write results to database
- -h, --help, -? print help (this message)
-
-Please note that where an argument expects a value, this is true for all
-alternative argument styles.
-
-=head1 DESCRIPTION
-
-This is a script to facilitate patching databases to the next schema version.
-It will connect to a database server and apply schema patches to all databases
-where the name matches a pattern. The pattern is a string that can be used in an
-'IN' clause in SQL (e.g. "%_core_%"; if you want to patch only a single
-database, use a pattern without % expansion, e.g. "homo_sapiens_core_38_36").
-
-If you only want to check which patches need to be applied, use --dry_run=1
-(best done in combination with --interactive=0).
-
-=head1 LICENCE
-
-This code is distributed under an Apache style licence:
-Please see http://www.ensembl.org/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
-<dev@ensembl.org>
-
-=cut
-
-# Should really add explicit --schema_type param to avoid applying core patches to non-core DBs
-# Could also validate this against meta schema.type = core|funcgen|variation
-
-use strict;
-use warnings;
-no warnings 'uninitialized';
-
-use FindBin qw($Bin);
-use vars qw($SERVERROOT);
-
-BEGIN {
- $SERVERROOT = "$Bin/../..";
- unshift(@INC, "$SERVERROOT/ensembl/modules");
-}
-
-use Getopt::Long;
-use Pod::Usage;
-use Bio::EnsEMBL::Utils::ConversionSupport;
-use DBI;
-
-$| = 1;
-
-my $support = new Bio::EnsEMBL::Utils::ConversionSupport($SERVERROOT);
-
-# parse options
-$support->parse_common_options(@_);
-$support->param('dbname', undef);
-$support->parse_extra_options(
- 'pattern|dbpattern=s',
- 'schema|dbschema=s',
- 'bindir=s',
- 'schema_type=s',
- );
-my @params = map { $_ unless ($_ =~ /dbname/) } $support->get_common_params;
-$support->allowed_params(
- @params,
- 'pattern',
- 'schema',
- 'bindir',
- 'schema_type'
-);
-
-if ($support->param('help') or $support->error) {
- warn $support->error if $support->error;
- pod2usage(1);
-}
-
-unless ($support->param('bindir')) {
- $support->param('bindir', '/usr/local/ensembl/bin');
-}
-
-# ask user to confirm parameters to proceed
-$support->confirm_params;
-
-# get log filehandle and print heading and parameters to logfile
-$support->init_log;
-
-$support->check_required_params(
- 'pattern',
- 'schema',
- 'schema_type'
-);
-
-my $schema_type = $support->param('schema_type');
-my %patch_dirs = (
- 'core' => "$SERVERROOT/ensembl/sql",
- 'funcgen' => "$SERVERROOT/ensembl-functgenomics/sql",
- 'variation' => "$SERVERROOT/ensembl-variation/sql",
- );
-
-#check schema_type is valid
-if(! (defined $schema_type && exists $patch_dirs{$schema_type})){
- $support->log_error('You must specify a valid --schema_type parameter e.g. core|variation|funcgen');
-}
-
-# connect to database
-my $dbh = $support->get_dbconnection;
-
-# read patches from file
-$support->log("Reading patches from file...\n");
-my $patchdir = $patch_dirs{$schema_type};
-my $schema = $support->param('schema');
-my @patches;
-
-opendir(DIR, $patchdir) or
- $support->log_error("Can't opendir $patchdir: $!");
-
-while (my $file = readdir(DIR)) {
- if ($file =~ /^patch_\d+_${schema}.*\.sql$/) {
- $support->log("$file\n", 1);
- push @patches, $file;
- }
-}
-
-$support->log("Done.\n\n");
-
-# get all database names that match pattern
-my ($sth, $sql);
-$sql = "SHOW DATABASES LIKE '".$support->param('pattern')."'";
-$sth = $dbh->prepare($sql);
-$sth->execute;
-
-# loop over databases
-while (my ($dbname) = $sth->fetchrow_array) {
- $support->log_stamped("$dbname\n");
-
- my $failure = 0;
- if ($support->user_proceed("\nPatch $dbname?")) {
-
- # check which patches have already been applied
- $sql = qq(SELECT meta_value FROM $dbname.meta WHERE meta_key = 'patch');
- my $sth1 = $dbh->prepare($sql);
- $sth1->execute;
-
- my %applied;
-
- while (my ($val) = $sth1->fetchrow_array) {
- my ($file) = split(/\|/, $val);
- $applied{$file} = 1;
- }
-
- # apply the missing ones
- foreach my $patch (sort @patches) {
- # if a patch has failed do not continue with other patches as there may be dependencies.
- if(!$failure){
- $support->log("$patch... ", 1);
-
- if ($applied{$patch}) {
- $support->log("already applied.\n")
-
- } elsif ($support->param('dry_run')) {
- $support->log("needs applying.\n")
-
- } else {
- $support->log("applying... ");
-
- my $cmd = $support->param('bindir')."/mysql".
- " -h ".$support->param('host').
- " -P ".$support->param('port').
- " -u ".$support->param('user').
- " -p".$support->param('pass').
- " $dbname < $patchdir/$patch";
-
- if (system($cmd) == 0) {
- $support->log("done.\n");
- } else {
- $support->log_warning("Error applying patch. Please check patch file.\n", 1);
- $failure = 1;
- }
-
- }
- }
- }
-
- } else {
- $support->log("Skipping on user's request.\n", 1);
- }
-
- $support->log("Done.\n\n");
-}
-
-# finish logfile
-$support->finish_log;
-