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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.
  4. To use in a publicly-facing context, see the configuration information below.

Configuration

Only two files are used to configure Omics Dashboard when deploying with Docker Compose: common.env, defines the environment variables in the application containers and .env defines the environment variables during the container build process. The following variables may be changed, but only OMICSSERVER, SECRET, MYSQL_PASSWORD, MYSQL_ROOT_PASSWORD, MODULEDIR and BRAND have to be changed in most installations.

Variable File Description
COMPUTESERVER common.env The url of the compute server. Only change if you are hosting a Cromwell server outside of the Docker Compose network.
SECRET common.env A secret used for securing passwords, tokens and sessions. You must change this for your installation to be secure.
BRAND common.env Some text displayed in the navigation bar of the app. Should be changed to your organization's name.
DATADIR common.env The path relative to the omics server to store data. Should usually not be changed
MODULEDIR common.env, .env The path relative to the omics server to store CWL tool definitions. Should usually not be changed
OMICSSERVER common.env, .env The url of the Omics Dashboard server relative to the end user (what you would enter into the browser).
MYSQL_DATABASE common.env The name of the MariaDB (or MySQL) database used by the Cromwell jobserver. Should usually not be changed.
MYSQL_USER common.env The name of the MariaDB (or MySQL) database user. Should usually not be changed
MYSQL_PASSWORD common.env, .env The password for the MariaDB (or MySQL) database used by the jobserver. Should be changed to a securely-generated secret.
MYSQL_ROOT_PASSWORD common.env The password for the MariaDB (or MySQL) database root user.
DB_URI common.env The URI of the database used by the omics service. By default, a SQLite database is created in the data directory
HOSTPORT .env The port on the host you want to access the service from. Should be consistent with OMICSSERVER

Documentation

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

Licensing

Omics-Dashboard is licensed under the terms of the MIT License.

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.

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

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