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README.md

Installation instructions

Install WGCNA package in R:

source("http://bioconductor.org/biocLite.R")
biocLite(c("AnnotationDbi", "impute", "GO.db", "preprocessCore"))
install.packages("WGCNA")

Clone git

git clone https://github.com/LUMC-BioSemantics/crosslinkWGCNA.git

In wgcna folder:

Checkout developtment branch: git checkout layout

In www folder:

Install npm if it is not installed.

Install required packages: npm install

Run the development web server: npm run dev

In api folder:

Set location of flask application: export FLASK_APP=app/__init__.py
Install dependencies:
pip install Flask-Session
pip install flask-cors --upgrade
sudo apt-get install python-scipy
pip install redis
pip install pandas
pip install rpy2==2.8.6
sudo apt-get install redis-server
Make sure that redis-server is running

Run flask application:
flask run

If errors: install any missing dependencies that are causing these errors.

Prepare data folder:

Create the data folder: mkdir /opt/wgcna

set write permission for user: sudo chown -R user:user /opt/wgcna
For help on chown, see for example: https://askubuntu.com/questions/49184/sudo-chown-r-rootmyusername-var-lib-php-session-what-should-i-put-in-usernam

Open webtool:

open localhost:4000 in google chrome.

Run instructions:

In www folder:

npm run dev

In api folder:

export FLASK_APP=app/__init__.py

flask run

Open webtool:

open localhost:4000 in google chrome.

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