Frequently Asked Questions
Please refer to corresponding Gen3 Documentation to create your first program and project.
Please make sure you inserted program
name in the URL, not
Please ensure you granted yourself permissions in the
user.yaml file. You can
find this file in the
Secrets folder within your Compose Services folder.
Follow provided in the file example to grant yourself relevant permissions. You
can find more information in the
Setting Up Users
Please ensure you are using
dbgap_accession_number value as an identifier for
auth_id field, not program’s
name or project’s
Don’t worry. The warning about connection not being private appears because
creds_setup.sh script generated self-signed SSL certificate to allow
microservices to communicate with each other without bypassing SSL verification.
Your browser can not verify this certificate. Once you install a trusted SSL
certificate instead of generated by our script, this warning will go away.
To configure Compose Services with your domain, please change the
field in the
fence_config.yaml file, and the
hostname field in the
You can add self-signed certificate to your trusted certificates. Steps may vary depending on Operating System you use.
config_folder variable sets the location of your
user.yaml file. If you
are using a local file, you can put any value - it won’t be used. If you are
using any of our
user.yaml files, then you may need to know which one. If you
are neither using ours nor local, you can also put a random value, and then
later when deploying kubernetes, you will be able to point the location of your
If you run
gen3 job run usersync changes should be picked up automatically.
If you don’t want to run that command every time you make changes to your
user.yaml, you can deploy the cronjob
gen3 job run usersync-cronjob and
kubernetes will check for changes every hour and update services accordingly.
You can override the default configuration in your commons by using
gitops.json file. Set your
gitops in your file
cdis-manifest/your-commons-name/manifest.json. Then create
cdis-manifest/your-commons-name/portal/gitops.json file. You can use this
as a template for your own
gitops.json file. Set navigation title and login
title at your choice. Then reroll portal with
After updating the Fence configuration, run
kubectl delete secret fence-config,
gen3 kube-setup-fence and roll Fence for configuration changes
to take effect with
gen3 roll fence.
You may need to hit the
Switch to Graph Model button in the upper right
Please refer to Cloud Automation documentation.
kubectl logs <name of pod> can show you corresponding errors in the logs.
First, restart Peregrine
gen3 roll peregrine and Sheepdog
gen3 roll sheepdog. After these two services restarted, please portal with
gen3 roll portal. Please note, if you are making significant changes to the dictionary,
you will also need to update
portal_app in the manifest.
Yes, you can update the manifest to use your version of the portal and use
gen3 kube-setup-portal or
gen3 roll portal to changes to take effect.
You can set the
global.portal_app setting in your manifest to the name of your
windmill configuration file and run
kubectl delete secret fence-config and
gen3 kube-setup-fence. If
you also updated the
user.yaml in the folder
apis_configs, you need to run
gen3 job run useryaml-job.
After you change
gen3 kube-setup-secrets and
gen3 job run usersync.
The Exploration page needs to be set up with Elastic Search using Guppy. Please refer to the relevant Guppy and Cloud Automation documentation, and see an Sample Configuration for the Guppy.
Please refer documentation about Creating New Dictionary, Data Types and Templates
You can use our dictionaryutils tool. You can find an example on how to generate JSON in the README