Skip to content

Latest commit

 

History

History
114 lines (81 loc) · 5.06 KB

README.md

File metadata and controls

114 lines (81 loc) · 5.06 KB

Custom Studios Examples

Example configurations for deploying custom Seqera Studio applications from a Git repository.

Do not merge studio configurations into master! Each studio has its own dedicated branch.

Repository Structure

This repository uses a branch-per-studio model (similar to nf-core/test-datasets). The master branch contains only this documentation. Each studio's configuration lives on its own branch with a .seqera/ directory containing the studio-config.yaml and Dockerfile required for launching Studios from a Git repository.

Available Studios

Branch Studio Description
marimo Marimo Reactive Python notebook environment
cellxgene CellxGene Interactive single-cell data visualization
streamlit Streamlit MultiQC visualization using Streamlit
shiny R Shiny Interactive data visualization with R Shiny
ttyd TTYD Web-based terminal with bioinformatics tools

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, ttyd)
  5. Select your compute environment
  6. Click Add then Start

Each branch contains a .seqera/ directory with:

  • studio-config.yaml — Studio configuration pointing to the Dockerfile
  • Dockerfile — Container definition with connect-client integration
  • Any supporting files required by the Dockerfile

Alternative Deployment: Pre-built Images

Each studio is also available as a pre-built container image:

ghcr.io/seqeralabs/custom-studios-examples/marimo:latest
ghcr.io/seqeralabs/custom-studios-examples/cellxgene:latest
ghcr.io/seqeralabs/custom-studios-examples/streamlit:latest
ghcr.io/seqeralabs/custom-studios-examples/shiny:latest
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.

Alternative Deployment: Wave CLI

You can also build any studio with the Wave CLI:

# Clone only the branch you need
git clone https://github.com/seqeralabs/custom-studios-examples.git --single-branch --branch <studio-name>

# Build with Wave
wave -f .seqera/Dockerfile --context .seqera --platform linux/amd64 --await --tower-token "$TOWER_ACCESS_TOKEN"

Cloning a Specific Studio

Due to the branch-per-studio model, we recommend cloning only the branch you need:

git clone https://github.com/seqeralabs/custom-studios-examples.git --single-branch --branch <studio-name>

To add another branch later:

git remote set-branches --add origin <studio-name>
git fetch

Environment Variables

Some studios support environment variable configuration:

Studio Variable Default Description
CellxGene DATASET_FILE s3://cellxgene_datasets/pbmc3k.h5ad Path to .h5ad dataset
CellxGene DATASET_TITLE PBMCs 3k test dataset Display title
CellxGene USER_DATA_DIR /user-data/cellxgene User data storage
CellxGene ANNOTATIONS_DIR /user-data/cellxgene Annotations storage
Shiny DATA_PATH s3://shiny-inputs/data.csv Path to CSV data file

Studios without listed variables (Marimo, Streamlit, TTYD) work with their default configurations.

Common Features

All studios in this repository:

  • Use the .seqera/ directory convention for Git-based Studio deployment
  • Include the required Seqera connect-client for platform integration
  • Support data mounting via datalinks in Studios
  • Are built for linux/amd64 platform compatibility
  • Use multi-stage Docker builds with connect-client

Documentation

Contributing

To add a new studio:

  1. Create a new branch from an empty root (orphan branch): git checkout --orphan <studio-name>
  2. Add a .seqera/ directory with studio-config.yaml and Dockerfile
  3. Add a README.md documenting the studio
  4. Push the branch
  5. Update this README on master to list the new studio