an example of using SqlCmd

docs/test_SqlCmd.conf

+# mini-pipeline for testing meta-parameter evaluation and SqlCmd in "external_db" mode
+
+my $cvs_root_dir      = $ENV{'HOME'}.'/work';
+
+    # family database connection parameters (our main database):
+my $pipeline_db = {
+    -host   => 'compara3',
+    -port   => 3306,
+    -user   => 'ensadmin',
+    -pass   => 'ensembl',
+    -dbname => "lg4_test_sqlcmd",
+};
+
+my $slave_db  = {
+    -host   => 'compara3',
+    -port   => 3306,
+    -user   => 'ensadmin',
+    -pass   => 'ensembl',
+    -dbname => "lg4_test_sqlcmd_slave",
+};
+
+return {
+        # pass connection parameters into the pipeline initialization script to create adaptors:
+    -pipeline_db => $pipeline_db,
+
+        # shell commands that create and pre-fill the pipeline database:
+    -pipeline_create_commands => [
+        'mysql '.dbconn_2_mysql($pipeline_db, 0)." -e 'CREATE DATABASE $pipeline_db->{-dbname}'",
+
+        'mysql '.dbconn_2_mysql($pipeline_db, 1)." <$cvs_root_dir/ensembl-hive/sql/tables.sql",
+        'mysql '.dbconn_2_mysql($pipeline_db, 1)." <$cvs_root_dir/ensembl-hive/sql/procedures.sql",
+
+        'mysql '.dbconn_2_mysql($pipeline_db, 0)." -e 'CREATE DATABASE $slave_db->{-dbname}'",
+    ],
+
+    -pipeline_wide_parameters => {  # these parameter values are visible to all analyses, can be overridden by parameters{} and input_id{}
+
+        'db_conn' => $slave_db, # testing the stringification of a structure here
+    },
+
+    -resource_classes => {
+         0 => { -desc => 'default, 8h',      'LSF' => '' },
+         1 => { -desc => 'urgent',           'LSF' => '-q yesterday' },
+    },
+
+    -pipeline_analyses => [
+        {   -logic_name => 'create_table',
+            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::SqlCmd',
+            -parameters => { },
+            -hive_capacity => 20, # to enable parallel branches
+            -input_ids => [
+                { 'sql' => 'CREATE TABLE distance (place_from char(40) NOT NULL, place_to char(40) NOT NULL, miles float, PRIMARY KEY (place_from, place_to))', },
+            ],
+            -rc_id => 1,
+        },
+
+        {   -logic_name => 'fill_in_table',
+            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::SqlCmd',
+            -parameters => {
+                'sql' => [ "INSERT INTO distance (place_from, place_to, miles) VALUES ('#from#', '#to#', #miles#)",
+                           "INSERT INTO distance (place_from, place_to, miles) VALUES ('#to#', '#from#', #miles#)", ],
+            },
+            -hive_capacity => 20, # to enable parallel branches
+            -input_ids => [
+                { 'from' => 'Cambridge', 'to' => 'Ely', 'miles' => 18.3 },
+                { 'from' => 'London', 'to' => 'Cambridge', 'miles' => 60 },
+            ],
+            -wait_for => 'create_table',
+            -rc_id => 1,
+        },
+    ],
+};
+