Commit 7819d7e3 authored by Leo Gordon's avatar Leo Gordon
Browse files

added a compara_db example

parent d32bf180
......@@ -109,9 +109,15 @@ __DATA__
standaloneJob.pl Bio::EnsEMBL::Hive::RunnableDB::FailureTest -no_write -time_RUN=2 -time_WRITE_OUTPUT=3 -state=WRITE_OUTPUT -value=2
# Run a job and re-direct its dataflow into tables:
standaloneJob.pl Bio::EnsEMBL::Hive::RunnableDB::JobFactory -inputfile foo.txt -delimiter '\t' -column_names "[ 'name', 'age' ]"
standaloneJob.pl Bio::EnsEMBL::Hive::RunnableDB::JobFactory -inputfile foo.txt -delimiter '\t' -column_names "[ 'name', 'age' ]" \
-flow_into "{ 2 => ['mysql://ensadmin:xxxxxxx@127.0.0.1:2914/lg4_triggers/foo', 'mysql://ensadmin:xxxxxxx@127.0.0.1:2914/lg4_triggers/bar'] }"
# Run a Compara job that needs a connection to Compara database:
standaloneJob.pl Bio::EnsEMBL::Compara::RunnableDB::ObjectFactory -compara_db 'mysql://ensadmin:xxxxxxx@127.0.0.1:2911/sf5_ensembl_compara_master' \
-adaptor_name MethodLinkSpeciesSetAdaptor -adaptor_method fetch_all_by_method_link_type -method_param_list "[ 'ENSEMBL_ORTHOLOGUES' ]" \
-column_names2getters "{ 'name' => 'name', 'mlss_id' => 'dbID' }" -flow_into "{ 2 => 'mysql://ensadmin:xxxxxxx@127.0.0.1:2914/lg4_triggers/baz' }"
=head1 SCRIPT-SPECIFIC OPTIONS
-help : print this help
......
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