Orthovenn3

Deploying OrthoVenn 3 via Rancher

OrthoVenn 3 is a web-based tool for whole-genome comparison across up to 12 species. It identifies orthologous gene clusters, visualizes overlaps via Venn diagrams, and provides functional enrichment analysis (GO terms and KEGG pathways) for selected gene subsets.

This guide outlines how to deploy, configure, and manage OrthoVenn 3 using the Rancher application catalog in Kubernetes.

You can run a desktop application by following the steps below.

Installation Steps

1.If you are not already logged in, log in to rancher.cloud.e-infra.cz, see Rancher section. 2. Navigate to Apps/Charts in the Rancher dashboard 3. Search for OrthoVenn 3 and install a new version (upper right corner).

4. Fill in the form:

   • namespace (do not use default, choose your namespace from the menu) and name

• login name and password

• data volume size — how much room you want for genomes and results

• how much CPU and memory the analyses may use

Click Install and wait. The first start takes a few minutes.

Access & URL Routing

You do not have to pick one. The app gets its address from the name you gave it and the namespace it went into:

https://<name>-<namespace>.dyn.cloud.e-infra.cz

• Example: An instance named ortho deployed in the mylab namespace is accessible at https://ortho-mylab.dyn.cloud.e-infra.cz.

• Alternative Suffixes: Depending on cluster policies, the domain suffix may end in .dyn.cloud.trusted.e-infra.cz. Check the Notes tab in Rancher post-deployment for the exact URL.

• TLS/SSL: Certificates are provisioned automatically via cert-manager; HTTPS is enabled by default.

Login In

OrthoVenn has no user accounts. Instead, the whole site asks for the login name and password you entered during install — the browser prompts for them the first time someone opens the page. Everyone shares that one login, so treat it as a door key rather than a personal account.

If you forget the password, reinstall or edit the app in Rancher and set a newone.

Storage

The application provisions two persistent volumes:

• a small one database volume for internal application data.
• a larger data volume for uploaded genomes, working files and finished results

The data volume handles the majority of the storage and cannot be downsized later If you anticipate working with large genomes or datasets, allocate more storage during installation than you think you will need.

Both volumes are retained automatically upon uninstallation to prevent accidental data loss. Reinstalling the app with the same name and namespace will reattach the existing volumes and restore your data.

Uninstallation & Cleanup

Delete Application: In Rancher, go to Installed Apps or running Pods, select OrthoVenn 3, and click Delete.

To permanently release the storage, navigate to Rancher’s Storage -> PersistantVolumeClaims section and manually delete the two associated Persistent Volume Claims (named with the suffixes -db and -home). Note that this deletion is irreversible.