Configure Your Galaxy Instance as a Custos Client
This page explains how to configure this feature as an administrator, for user-specific docs, please refer to the Use page.
Custos is an NSF-funded project, backed by open source software that provides science gateways such as Galaxy with single sign-on, group management, and management of secrets such as access keys and OAuth2 access tokens. With Galaxy, Custos allows users to login to Galaxy without having to (explicitly) create a Galaxy user account while being able to login choosing from more than 3,000 available Identity Providers (IdPs). Many of the academic institutions from around the world are supported allowing users to link their institutional identities with a Galaxy account.
To set up a Galaxy instance to work with Custos, it is necessary to enable
OIDC-based login for Galaxy. To do this, follow the instructions for enabling
Next, it is necessary to register your Galaxy instance as a client of Custos.
The following section demonstrates how to do that. Finally, you need to
configure Custos as an IdP provider in Galaxy by editing
config/oidc_backends_config.xml. An example file is provided below.
Development of a portal for registering new Custos clients is currently in progress. In the meantime, you can register a client directly through a REST API. This can be accomplished using a platform such as Postman.
To register a new Galaxy client with Custos, make a POST request with the following body, replacing information with your relevant data:
- URI : https://custos.scigap.org:/apiserver/tenant-management/v1.0.0/oauth2/tenant
- Method : POST
- Body :
client_name:John Doe University requester_email:email@example.com admin_username:johndoe admin_first_name:John admin_last_name:Doe admin_email:firstname.lastname@example.org contacts: redirect_uris:[https://jduniversity.edu/galaxy/authnz/custos/callback] domain:jduniversity.edu admin_password:1234 client_uri:jduniversity.edu scope:email profile openId org.cilogon.userinfo application_type:web
The Domain should be the main address that users will use to get to your instance of Galaxy.
For the Redirect URIs field, you need to enter your instance’s OIDC redirect URI, which is in the following template:
See this section for details.
After making the POST request, you should get a response containing your
Client Secret; note this info! You will need it for the Galaxy configuration.
Finally, to have your client activated, send an email to email@example.com with your
Once we have an activated client ID and client secret from Custos, we need to
configure Galaxy. As a first step, make sure to enable OIDC
login. After setting up
config/oidc_config.xml, which is common to multiple IdPs, you need to
config/oidc_backends_config.xml. The following is an example of a
configuration. Note that the redirect_uri must match what as included as
the callback URL during your Custos client registration. Also note that
127.0.0.1 are not the same; if you register
access your Galaxy via
localhost, the redirect will not work. The client ID
and client secret are unique to your installation of Galaxy and were obtained
during client registration.
<?xml version="1.0"?> <OIDC> <provider name="Custos"> <url>https://custos.scigap.org/apiserver/identity-management/v1.0.0/</url> <client_id>custos-xmn3092m8tkh7546hv76-10000001</client_id> <client_secret>15Ur37stVGwvONALNjjq89ezRXxoKuunFzvEeTDY</client_secret> <redirect_uri>http://jduniversity.edu/galaxy/authnz/custos/callback</redirect_uri> </provider> </OIDC>
The above configuration includes the default OIDC configuration
as we as the required
url tag is a required Custos configuration. It provides a unique url
for the Custos service. The hosted public Custos service is available at the
URL included in the sample configuration above.
ca_bundle tag is optional. The value for this tag is an absolute path
to a trusted CA certificate file or directory to use when verifying Custos
authorization server. If this option is used, it is also necessary to set the
well_known_oidc_config_uri tag is optional and allows you to override the
default Custos well-known URL to point to a different instance.
enable_idp_logout is an optional boolean tag. If set, Galaxy will log out
the user from the IdP (eg, if a user used Google so authenticate, the user will
be logged out of Google as well as Galaxy). For this option to work, the
redirect_url during the client registration
above needs to specify a wild
card instead of the specific path (eg,
Having set this configuration, (re)start Galaxy and the
Sign in with Custos
feature will become available. The login page should look as follows:
For the end-user documentation of how to use the Custos login now that it has been configured, take a look at the end-user page.