diff --git a/misc-scripts/stable_id_lookup/README b/misc-scripts/stable_id_lookup/README index f5ef74fee89a3cf0135c4720b6a52e9f1ddc5818..a84d0422e9fbedb365cfa71049e5973c328b2408 100644 --- a/misc-scripts/stable_id_lookup/README +++ b/misc-scripts/stable_id_lookup/README @@ -1,7 +1,7 @@ The stable_id database is used by the Registry method get_species_and_object_type(). EnsEMBL REST API heavily relies on this method. -The database can be created on one of the staging servers once all the release databases, which contain +The database can be created once all the release databases, which contain stable_ids to be copied into the stable_id database, are ready. Currently the following stable ids are copied: @@ -33,7 +33,12 @@ RELEASE=88 DIR=ensembl/misc-scripts/stable_id_lookup cd $DIR -bsub -q production-rh7 -M 700000 -R'select[mem>700] rusage[mem=700]' -o stable_id_lookup.out -e stable_id_lookup.err perl populate_stable_id_lookup.pl \ --lhost mysql-xxx-dev-x.ebi.ac.uk -luser xxxx -lpass xxxx -lport 4484 -dbname ensembl_stable_ids_88 -create -host mysql-ens-xxx-1.ebi.ac.uk -user xxx -port 4519 -version 89 -create_index +bsub -q production-rh7 -M 700 -R'select[mem>700] rusage[mem=700]' -o stable_id_lookup.out -e stable_id_lookup.err perl populate_stable_id_lookup.pl \ +-lhost mysql-xxx-dev-x.ebi.ac.uk -luser xxxx -lpass xxxx -lport 4484 -dbname ensembl_stable_ids_${RELEASE} -create -host mysql-ens-xxx-1.ebi.ac.uk -user xxx -port 4519 -version ${RELEASE} -create_index + +-luser,lpass,lhost,lport = lookup credentials, or the dev server account with write permissions. +-user,pass,host,port = read-only credentials for staging servers. This is where the stable IDs come from. +-dbname = name of new lookup database to create on the server defined by -lhost For release 89, the job consumed around 100MB of memory and took around 3 mins to run for ensembl on the EBI cluster. +For release 92, the job took around 8 minutes.