genome-nexus/genome-nexus

Name: genome-nexus

Owner: genome-nexus

Description: Interpreting cancer genomics data

Created: 2015-09-16 14:16:27.0

Updated: 2017-08-18 20:25:47.0

Pushed: 2017-12-15 01:03:01.0

Homepage: http://genomenexus.org

Size: 15961

Language: Java

GitHub Committers

User	Most Recent Commit	# Commits
n1zea144	2016-03-21 14:05:29.0	7
JianJiong Gao	2016-07-27 22:21:19.0	3
Ino de Bruijn	2018-03-21 19:30:14.0	72
pieterlukasse	2018-01-18 10:46:30.0	1
Onur Sumer	2018-03-21 18:46:12.0	66
Robert Sheridan	2017-10-16 22:14:42.0	2
Zachary Heins	2017-07-24 19:51:49.0	6
angelicaochoa	2017-10-25 13:13:22.0	6
athum	2017-08-17 21:05:13.0	1

Other Committers

User	Email	Most Recent Commit	# Commits

README

| branch | master | rc | | — | — | — | | status | | |

Genome Nexus

Genome Nexus, a comprehensive one-stop resource for fast, automated and high-throughput annotation and interpretation of genetic variants in cancer. Genome Nexus will integrate information from a variety of existing resources, including databases that convert DNA changes to protein changes, predict the functional effects of protein mutations, and contain information about mutation frequencies, gene function, variant effects, and clinical actionability.

Three goals:

1. Data collection from various annotation sources
2. Integration of heterogeneous information into a harmonized structure and programmatic interface
3. Dissemination of the diverse information in a hierarchical digestible way for interpreting variants and patients.

Run

Alternative 1 - run genome-nexus and mongoDB in docker containers

Run with docker (assumes mvn installed locally):

 -DskipTests clean install
er compose up --build

The mongo image genomenexus/gn-mongo comes with all the required tables initialized.

Alternative 2 - run genome-nexus locally, but mongoDB in docker container

e genomenexus/gn-mongo images comes with all the required tables imported
ange latest to different version if necessary (only need to run this once)
er run --name=gn-mongo --restart=always -p 27017:27017 -d genomenexus/gn-mongo:latest 
 -DskipTests clean install
 -jar web/target/web-*.war

Alternative 3 - install mongoDB locally and run with local java

Install mongoDB manually. Then follow instructions in genome-nexus-importer to initialize the database.

After that run this:

clean install
 -jar web/target/web-*.war

Update data

If you need to update the data files see genome-nexus-importer

Programmatic access through R/Python

See notebooks/