readme.md

iDEP: Integrated Differential Expression and Pathway analysis

iDEP is a Shiny app for analyzing RNA-seq or other transcriptomic data. See documentation and paper. Based on annotation of 220 animal and plant genomes in Ensembl BioMart as of 6/4/2018. Additional data from KEGG, Reactome, MSigDB (human), GSKB (mouse) and araPath (arabidopsis). For feedbacks or data contributions (genes and GO mapping of any species), please contact us, or visit our homepage. Send us suggestions or any error message to help improve iDEP.

iDEP is a web application hosted at http://bioinformatics.sdstate.edu/idep/

Local installation of this software is possible through steps below. But it is not supported or updated freqently.

Requirements

• Storage should be more than 200GB
• Memory should be more than 2GB

Prerequisites

• git Installation Guide

• docker community edition (win10 above and MacOS)Installation Guide https://docs.docker.com/engine/installation/linux/docker-ce/debian/#install-using-the-repository

• • docker toolbox (win7)

Install docker and docker-compose

More detail information

• Installation

Download database files for running iDEP locally can be downloaded at

https://doi.org/10.5281/zenodo.1451847.

Quick Start

From your local machine Make clone

> git clone https://github.com/iDEP-SDSU/idep.git

The following command starts containers from docker-compose.yml. The R server listening for HTTP connections on port 3838

> docker-compose up -d

Check [localhost:3838] (http://localhost:3838/idep)

Advanced Use (docker container base)

• Manage Docker Compose
• Manage Docker Image and Container

Build Docker image

You can build docker image of

docker build -t {name} .

Run Shiny Server Docker Image

docker run --rm -p 3838:3838 \
    -v $(pwd)/shinyapps/:/srv/shiny-server/ \
    -v $(pwd)/shinylog/:/var/log/ \
    idep/early

docker run --rm -p 3838:3838 idep/early

You can bring everything down, removing the containers entirely, with the down command. Pass --voluems to also remove the data volume.

> docker-compose down --volumes

Documentation

https://idepsite.wordpress.com/ http://docs.rstudio.com/shiny-server/

Resources

Docker-Compoer documentation

https://docs.docker.com/compose/reference/overview/

Shiny Server Log

https://support.rstudio.com/hc/en-us/articles/115003717168-Shiny-Server-Error-Logs

Install required packages

open docker terminal

> Rscript librarySetup.R

Production server

docker-compose -f docker-compose.yml -f docker-compose.do.yml up -d

Proxy https://gist.github.com/netdesk/c1db2985b542f9916995139318e5a7ce