Reproducible Research Platform Minimal Template Player Bundle

RRP Minimal Template Reproducible Research Platform project minimal template (cookiecutter). Overview Adopt this minimal template (cookiecutter) RRP project repository for your projects. The main outcome of this example is: How to setup an RRP project Features Computation environment: Defines the computational environment. Integration with RRP and openBIS ELN--LIMS: Mounts data form the RDMS openBIS in RRP. Installation Prerequisites Local Docker installation. Steps Download and extract the .zip file Run the play script for your operating system Linux / macOS: play Windows: play.bat or play.ps1 Usage 1. Specify computational environment In a .binder/apt.txt file you specify system libraries and binaries nano # a text editor git-all # git support In a .binder/requirements.txt file you specify python packages (e.g. numpy) and extensions as well as minimal or exact versions for reproducibility. Note you can also use conda environment.yml files for this. Below an example for requirements.txt jupyterlab-git==0.44.0 jupyterlab==4.3.4 In a .binder/runtime.txt file you specify the Python (R, ...) version. python-3.11 2. Mount data In a .rrp/datasets.yaml file specify the permIDs of your data to be mounted. The data is then mounted directly in a folder termed openbis. You can mount additional data directly within RRP on the fly also later. Note you can also create a new RRP project without specifying any data (initially). server-url: "openbis-xxx.ethz.ch" # Specify your RDMS instance of openBIS destinations: "raw_data": # Name of a folder within /openbis for e.g. raw data. - "20250403175140454-199020" # PermID of the dataset(s) "other_data": # Name of another folder within /openbis, for e.g., other data. - "20191211114115370-36980" # PermID of the dataset(s) Workflow Overview Define computational environment: Specify the computational environment. Define data: Specify which data to use from the RDMS openBIS. Run RRP project: Create a new RRP project on the RRP platform from a Git repository. Manage project: Work in the project folder e.g. add analysis scripts, mount code etc. Directory Structure ├── .binder/ # Environment specifications, LaTeX version, packages etc. ├── .rrp/ # Specification of required data from RDMS openBIS ELN-LIMS (e.g. data) ├── LICENSE # License └── README.md # This file Contributing We welcome contributions to improve this repository! Please follow these steps: Fork the repository. Create a new branch for your feature or bug fix. Submit a pull request with a clear description of your changes. Authors and acknowledgment Andreas P. Cuny, ETH Zurich initial implementation License This project is licensed under the Apache 2.0 License. See LICENSE file for details. Copyright © 2020-2025 ETH Zurich, Andreas P. Cuny, D-BSSE, CSB Group References https://rrp.ethz.ch/