diff --git a/AGENTS.md b/AGENTS.md index a869523..d8199dc 100644 --- a/AGENTS.md +++ b/AGENTS.md @@ -4,7 +4,7 @@ Guidance for AI coding agents working in this repository. ## Repository overview -This is **Seqera Labs Custom Studios Examples** — a collection of Docker-based [Seqera Platform Studios](https://docs.seqera.io/platform-cloud/studios/overview) reference environments. Each studio is a standalone container image (Marimo, CellxGene, Streamlit, R Shiny, Shinyngs, TTYD). There is no root-level package manager, monorepo build, or docker-compose stack. +This is **Seqera Labs Custom Studios Examples** — a collection of Docker-based [Seqera Platform Studios](https://docs.seqera.io/platform-cloud/studios/overview) reference environments. Each studio is a standalone container image (Marimo, CellxGene, Streamlit, R Shiny, Shinyngs, TTYD, and the branch-only desktop studios QuPath/KasmVNC and Selkies Webtop). There is no root-level package manager, monorepo build, or docker-compose stack. The `master` branch holds documentation and example directories. Deployable studio configs (`.seqera/studio-config.yaml`) live on dedicated git branches per studio. diff --git a/README.md b/README.md index 6330ba8..6e4e703 100644 --- a/README.md +++ b/README.md @@ -18,13 +18,15 @@ This repository uses a **branch-per-studio** model (similar to [nf-core/test-dat | [`shiny`](https://github.com/seqeralabs/custom-studios-examples/tree/shiny) | R Shiny | Interactive data visualization with R Shiny | | [`shinyngs`](https://github.com/seqeralabs/custom-studios-examples/tree/shinyngs) | Shinyngs | RNA-seq exploration with the `shinyngs` R package | | [`ttyd`](https://github.com/seqeralabs/custom-studios-examples/tree/ttyd) | TTYD | Web-based terminal with bioinformatics tools | +| [`kasmvnc-qupath`](https://github.com/seqeralabs/custom-studios-examples/tree/kasmvnc-qupath) | QuPath | Bioimage analysis desktop app streamed with KasmVNC | +| [`selkies-webtop`](https://github.com/seqeralabs/custom-studios-examples/tree/selkies-webtop) | Selkies Webtop | Full Debian XFCE desktop streamed with Selkies | ## Quick Start: Launch from Git Repository 1. Navigate to **Studios** > **Add Studio** in your Seqera Platform workspace 2. Select **Git repository** as the source 3. Enter the repository URL: `https://github.com/seqeralabs/custom-studios-examples` -4. Select the branch for the studio you want (e.g., `marimo`, `cellxgene`, `streamlit`, `shiny`, `shinyngs`, `ttyd`) +4. Select the branch for the studio you want (e.g., `marimo`, `cellxgene`, `streamlit`, `shiny`, `shinyngs`, `ttyd`, `kasmvnc-qupath`, `selkies-webtop`) 5. Select your compute environment 6. Click **Add** then **Start** @@ -35,7 +37,7 @@ Each branch contains a `.seqera/` directory with: ## Alternative Deployment: Pre-built Images -Each studio is also available as a pre-built container image: +These studios are also available as pre-built container images: ``` ghcr.io/seqeralabs/custom-studios-examples/marimo:latest @@ -48,6 +50,8 @@ ghcr.io/seqeralabs/custom-studios-examples/ttyd:latest To use a pre-built image, select **Prebuilt container image** instead of **Git repository** when adding a Studio. +The desktop studios (`kasmvnc-qupath`, `selkies-webtop`) have no pre-built image; add them from their Git branch, or build them with the Wave CLI. + ## Alternative Deployment: Wave CLI You can also build any studio with the [Wave CLI](https://docs.seqera.io/wave/): @@ -89,6 +93,8 @@ Some studios support environment variable configuration: Studios without listed variables (Marimo, Shinyngs, Streamlit, TTYD) work with their default configurations. +The desktop studios expose display and streaming variables instead of data paths — QuPath's interface scale and KasmVNC frame rate and compression, and Selkies' DPI and startup behavior. Those are documented in the [`kasmvnc-qupath`](https://github.com/seqeralabs/custom-studios-examples/blob/kasmvnc-qupath/README.md) and [`selkies-webtop`](https://github.com/seqeralabs/custom-studios-examples/blob/selkies-webtop/README.md) branch READMEs. + ## Common Features All studios in this repository: