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docs(seqera-ai): align Enterprise Co-Scientist docs for 26.1#1381

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llewellyn-sl wants to merge 2 commits intoenterprise-26.1-documentationfrom
26-1-docs-update
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docs(seqera-ai): align Enterprise Co-Scientist docs for 26.1#1381
llewellyn-sl wants to merge 2 commits intoenterprise-26.1-documentationfrom
26-1-docs-update

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Summary

  • Align Platform Enterprise Co-Scientist docs with the Cloud docset for the Enterprise 26.1 release.
  • Add Enterprise guidance for skills, modes, coding-agent integrations, Nextflow LSP, projects, and usage/cost behavior.
  • Rewrite the Enterprise Seqera AI install page with current MCP, agent-backend, portal-web, Redis, MySQL, Bedrock, Anthropic direct, AgentCore, OIDC, and CLI guidance.

Validation

  • git diff --check
  • Parsed platform-enterprise_docs/enterprise-sidebar.json
  • Targeted stale-string scans for Cloud-only credits/install wording and old Helm chart paths.

Notes

  • This is the public-docs PR that should get the closest release-doc review.

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netlify Bot commented May 4, 2026

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```bash
export SEQERA_AUTH_DOMAIN=https://cloud.seqera.io/api
export SEQERA_AUTH_DOMAIN=https://platform.example.com/api
export SEQERA_AUTH_CLI_CLIENT_ID=seqera_ai_cli
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Suggested change
export SEQERA_AUTH_CLI_CLIENT_ID=seqera_ai_cli

this doesn't seem to be needed

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I added these 4 to my shell when trying to get the CLI working. TBD if they were all necessary:

- `SEQERA_AI_BACKEND_URL`
- `SEQERA_AUTH_DOMAIN`
- `SEQERA_AUTH_CLI_CLIENT_ID`
- `TOWER_ACCESS_TOKEN`

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Commented on the parts of this PR which touched upon deployment. I did not review the "how to use the CLI" since this was not part of my efforts last week.

Comment thread platform-enterprise_docs/enterprise/install-seqera-ai.md Outdated
- **Token encryption key** for encrypting sensitive tokens at rest. Generate with:
- Seqera Platform Enterprise 26.1 or later deployed with the [Seqera Platform Helm chart](./platform-helm.md).
- Helm v3 and `kubectl` installed locally.
- DNS names and TLS certificates for the Platform, agent backend, MCP server, and portal web interface hosts.
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If created manually, where are they getting the FQDNs from? Having to look at the Helm chart config?

- Seqera Platform Enterprise 26.1 or later deployed with the [Seqera Platform Helm chart](./platform-helm.md).
- Helm v3 and `kubectl` installed locally.
- DNS names and TLS certificates for the Platform, agent backend, MCP server, and portal web interface hosts.
- Access to pull the `agent-backend`, `mcp`, and `portal-web` images from `cr.seqera.io`, or mirrored copies in your internal registry.
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Define repo? How does this align to the comments @bebosudo made today about the new proxy sites?

- Helm v3 and `kubectl` installed locally.
- DNS names and TLS certificates for the Platform, agent backend, MCP server, and portal web interface hosts.
- Access to pull the `agent-backend`, `mcp`, and `portal-web` images from `cr.seqera.io`, or mirrored copies in your internal registry.
- A MySQL 8 database for the agent backend. You can use the same MySQL instance as Platform with a separate database and user, or a separate instance.
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Minor version? I assume we want 8.4?

- DNS names and TLS certificates for the Platform, agent backend, MCP server, and portal web interface hosts.
- Access to pull the `agent-backend`, `mcp`, and `portal-web` images from `cr.seqera.io`, or mirrored copies in your internal registry.
- A MySQL 8 database for the agent backend. You can use the same MySQL instance as Platform with a separate database and user, or a separate instance.
- A Redis 7 instance for agent backend task coordination.
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Minor version? 7.2.x or something else?
Talk about Valkey support?

- Keep the agent backend token encryption key stable across upgrades. Changing it prevents the backend from decrypting existing encrypted values.
- MCP uses the user's Platform token to call Platform APIs. The agent backend does not need a separate long-lived Platform service credential for user-scoped tool calls.
- Use separate MySQL credentials for the agent backend database.
- Enable Redis TLS and MySQL TLS when your managed services require encrypted connections.
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See earlier comment about Valkey

See [Authentication](./authentication.md) for a comprehensive authentication guide.

If you are testing a development build of the CLI against the hosted production Seqera AI service, see [Install Seqera AI](../enterprise/install-seqera-ai.md#connect-the-cli-to-seqera-ai) for the required environment variables.
For Enterprise deployments, set `SEQERA_AI_BACKEND_URL` to your organization's agent backend before you start Co-Scientist. See [Authentication](./authentication.md#connect-to-an-enterprise-backend) for the full environment variable reference.
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Is this on the Platform config page?

Comment thread platform-enterprise_docs/seqera-ai/index.md
### npm install

```bash
npm install -g seqera
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Pretty sure I saw this covered somewhere else too? (Maybe that was the internal docs rather than external)?

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They're in the Enterprise installation docs and this is the CLI installation section so it's somewhat duplicated.

@@ -0,0 +1,112 @@
---
title: "Modes"
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@gwright99 gwright99 May 4, 2026

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Did not do this as part of install. Not commenting.

@justinegeffen justinegeffen changed the base branch from master to enterprise-26.1-documentation May 4, 2026 14:23
Signed-off-by: Justine Geffen <justinegeffen@users.noreply.github.com>
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4 participants