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Unverified Commit fd2b45b5 authored by Kieron Taylor's avatar Kieron Taylor Committed by GitHub
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Minor amendments to populate_stable_id_lookup.pl README

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The stable_id database is used by the Registry method get_species_and_object_type(). The stable_id database is used by the Registry method get_species_and_object_type().
EnsEMBL REST API heavily relies on this method. 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. stable_ids to be copied into the stable_id database, are ready.
Currently the following stable ids are copied: Currently the following stable ids are copied:
...@@ -33,7 +33,12 @@ RELEASE=88 ...@@ -33,7 +33,12 @@ RELEASE=88
DIR=ensembl/misc-scripts/stable_id_lookup DIR=ensembl/misc-scripts/stable_id_lookup
cd $DIR cd $DIR
bsub -q production-rh7 -M 700000 -R'select[mem>700] rusage[mem=700]' -o stable_id_lookup.out -e stable_id_lookup.err perl populate_stable_id_lookup.pl \ bsub -q production-rh7 -M 700 -R'select[mem>700] rusage[mem=700]' -o stable_id_lookup.out -e stable_id_lookup.err perl populate_stable_id_lookup.pl \
-lhost mysql-xxx-dev-x.ebi.ac.uk -luser xxxx -lpass xxxx -lport 4484 -dbname ensembl_stable_ids_88 -create -host mysql-ens-xxx-1.ebi.ac.uk -user xxx -port 4519 -version 89 -create_index -lhost mysql-xxx-dev-x.ebi.ac.uk -luser xxxx -lpass xxxx -lport 4484 -dbname ensembl_stable_ids_${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 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.
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