Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
E
ensembl
Manage
Activity
Members
Labels
Plan
Issues
0
Issue boards
Milestones
Iterations
Wiki
Requirements
Jira
Code
Merge requests
1
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Snippets
Locked files
Build
Pipelines
Jobs
Pipeline schedules
Test cases
Artifacts
Deploy
Releases
Package Registry
Container Registry
Operate
Environments
Terraform modules
Monitor
Incidents
Service Desk
Analyze
Value stream analytics
Contributor analytics
CI/CD analytics
Repository analytics
Code review analytics
Issue analytics
Insights
Help
Help
Support
GitLab documentation
Compare GitLab plans
Community forum
Contribute to GitLab
Provide feedback
Terms and privacy
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
ensembl-gh-mirror
ensembl
Commits
fd2b45b5
Unverified
Commit
fd2b45b5
authored
7 years ago
by
Kieron Taylor
Committed by
GitHub
7 years ago
Browse files
Options
Downloads
Patches
Plain Diff
Minor amendments to populate_stable_id_lookup.pl README
parent
0567925c
No related branches found
Branches containing commit
No related tags found
Tags containing commit
No related merge requests found
Changes
1
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
misc-scripts/stable_id_lookup/README
+8
-3
8 additions, 3 deletions
misc-scripts/stable_id_lookup/README
with
8 additions
and
3 deletions
misc-scripts/stable_id_lookup/README
+
8
−
3
View file @
fd2b45b5
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.
This diff is collapsed.
Click to expand it.
Preview
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment