MicroArray Dev Environment Setup
Prerequisite System Packages
| Component | Version | Note |
|---|---|---|
| R | v3.4.4 | Download on official website: https://www.r-project.org/ |
| devtools | latest | R -e "install.packages('devtools', repo='http://cran.r-project.org')" |
| Node.js (with npm) | v.8.11.3 or latest | |
| forever | latest | npm install forever -g |
| xvfb | latest | X virtual framebuffer is a display server implementing the X11 display server protocol (for microarray plots). |
Node Modules
Server: To install server dependencies, navigate to the root of the project and execute:
$ npm install
Client: To install client dependencies, navigate to the /client folder and run the same command
Forever Module: Install the forever module globally:
$ npm install forever -g
R Dependencies
All required R dependencies are defined in setup.R.
To install the R dependencies, navigate to /setup/setup.R and execute:
$ Rscript setup.R
Configuaration
Navigate to /config/index.js and update the setting variable path to microarray_setting-local.json, which is also found in the same folder.
Modify server settings in microarray_setting-local.json if needed.
From the project root, navigate one directory up to the /data folder. Create folder if it doesn't exist.
Place files from https://github.com/CCBR/MicroArrayPipeline/tree/master/mpstr_configuration_files into the /data folder.
Start
To start server, navigate to root of project and execute:
$ node index.js
To start the client, navigate to the /client folder and execute:
$ npm start