A software toolkit for the interconversion of standard data models for phenotypic data

Documentation: https://cnag-biomedical-informatics.github.io/convert-pheno-ui

Web APP Playground: https://convert-pheno.cnag.cat

CLI Source Code: https://github.com/cnag-biomedical-informatics/convert-pheno

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convert-pheno-ui is a web-interface for the CPAN's module Convert::Pheno which is a software toolkit for the interconversion of standard data models for phenotypic data.

The module will be uploaded to CPAN once the paper is submitted.

Getting Started

General pre-requisite:

• Ideally a unix (GNU/Linux, MacOS) based distribution. Windows with WSL (Windows Subsystem for Linux) enabled or Docker Deskop should work as well - not tested

• Docker and Docker compose installed

Quick Start

no SSL and user authentication 0. git clone this repo and then navigate into the folder convert-pheno-ui

1. rename the file example.env to .env and fill in the variables
2. Run docker compose up -d
3. Open your browser and go to http://localhost:4173

For self-hosters:

SSL and keycloak-based user authentication

Convert-Pheno is designed to be run as a collection of microservices. Please consult dev_docs/how_to_self_host_w_keycloak_login_enabled.md how to prepare your environment and run the services.

CITATION

The author requests that any published work that utilizes Convert-Pheno-UI includes a cite to the the following reference:

Rueda, M; Leist, IC et al., (2023). Convert-Pheno: A software toolkit for the interconversion of standard data models for phenotypic data [Software]. Available from https://github.com/cnag-biomedical-informatics/convert-pheno

AUTHOR

Written by Ivo Christopher Leist, PhD student at CNAG https://www.cnag.crg.eu.

COPYRIGHT AND LICENSE

Copyright (C) 2022-2023, Ivo Christopher Leist - CNAG.

GPLv3 - GNU General Public License v3.0