Xena-Analysis-Grails

Analysis-server for XenaGoWidget.

Allows analysis of arbitrary GMT files and samples against existing cohorts.

Setup

Currently no easy way to add, but setup Postgres to run locally with no username / password and to create the database xena-analysis.

However, we can configure other database relatively easily by editing the application.yml file.

Setup

• Install jdk8+

• Install Postgresql and configure in application.yml

To download all of the tpm files you need to run the unit tests:

./gradlew test-app 

Once downloaded the tests will be fast.

• Install R 4.0 +

Example for Ubuntu 16 (https://cran.r-project.org/bin/linux/ubuntu/README.html)

sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu xenial-cran40/'
sudo apt-get update
sudo apt-get install r-base

• Install R dependencies

At the top-level directory enter the R console:

 if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
 BiocManager::install("viper")
 install.packages("jsonlite")
 install.packages("stringr")
 install.packages("digest")
 install.packages("R.utils")

Quit and save the workspace.

Running

./gradlew run-app

Testing

./gradlew build