A tool for managing (primarily numeric) multiomics data such as microarray data, spectroscopy, etc.
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README.md

Omics Dashboard

A multiuser web-based data management and pipelining tool for systems biology workflows.

Omics Dashboard consists of a web service for managing data and workflows, and the Cromwell workflow engine from the Broad Institute for executing CWL (and eventually WDL) workflows. Omics Dashboard can be deployed from bare metal or various cloud services and is primarily intended for managing "small" metabolomics datasets (< 1 GB), though it eventually can be modified to deal with larger data. Omics Dashboard can accomodate multiple users with controlled access to data.

Getting Started

Omics Dashboard can be deployed in several ways. The easiest way is via Docker Compose.

On any machine with Docker and Docker Compose:

  1. Copy .env-example to .env and change the MODULEDIR variable to match the location of the repo's modules directory.
  2. Copy common-example.env to common.env. If you intend to deploy Omics Dashboard on a publicly-accessible server, you should change MYSQL_PASSWORD, MYSQL_ROOT_PASSWORD and SECRET to secure passwords.
  3. Run docker-compose up from the root of the repo and navigate to localhost:8080/omics/. The default username is admin@admin.admin and the default password is password. You should change the email address and password of this default user or create a new user, grant the user admin privelege, then delete the default user as the new user.

Documentation

Documentation for Omics Dashboard is located on the wiki of the GitHub repository.

Licensing

Omics-Dashboard is licensed under the terms of the AGPL v3. This is a very restrictive and "infectious" license. Since the configuration for Omics-Dashboard frequently involves changing the source code itself, it may not be possible to use Omics-Dashboard without making your modifications available to all users of your deployment. If this presents a problem, please contact the maintainers. Licensing under more permissive terms is available upon request and will most likely be granted for nearly any use case outside of operating Omics-Dashbaord as a commercial service.

Bug Reports & Feature Requests

We use GitHub issues to track public bugs. Report a bug by opening a new issue. Good issues should follow the templates provided.