ExpressVis-docker

Description

The project contains all necessary files for deploying ExpressVis (https://omicsmining.ncpsb.org.cn/ExpressVis/home) with Docker. Users can easily deploy ExpressVis locally or in their own server.

Prerequisite

1. Install Docker and docker-compose

2. Download ExpressVis.database.zip from ftp(ftp://omicsmining.ncpsb.org.cn/pub). Unzip the data and place them in a directory. You can download ftp data using filezilla.

3. Change R mirror. By default, installing R packages will use CRAN mirror "https://mirrors.tuna.tsinghua.edu.cn/CRAN" and bioconductor mirror "https://mirrors.tuna.tsinghua.edu.cn/bioconductor". Installing R packages will take a long time. You would better change them according to your location in the R code files that starts with install.

Deploy ExpressVis

1. Clone this project

   git clone https://github.com/OmicsMining/ExpressVis-docker.git

2. Change to ExpressVis-Docker directory

   cd ExpressVis-docker

3. Change database path in docker-compose.yml file.

   change '/user/annotationDatabasePath' to your database directory(from prerequisite 2) in setion djangoserver/volumes and section nginx/volumns/

4. Build intermediate image rserverbase. This image will be used in all R-based servers.

   cd ./rServerBase
   docker build -t rserverbase .
   

5. Build docker image rdiffbase. Rdifbase image will be used in rdiffServer image. Docker installs all necessary Microaray annotation packages and so building rdiffbase will take a long time. We recommend users only install Microarray packages they requires. By default, the Microarray packages in this project are just a few packages for test. Users can change the packages to be installed in ./rdiffbase/annoPackagesInfo/**.txt files. MicroarrayPackages.zip file that contains all Microarray packages infos can be downloaded from ftp(ftp://omicsmining.ncpsb.org.cn/pub).

   cd .. # Go back the root directory
   cd ./rdiffbase       
   docker build -t rdiffbase .
   

6. Build images and run containsers using docker-compose

   cd .. # Go back to the root directory of ExpressVis-docker from ./diffBase
   docker-compose up -d
   

7. Open ExpessVis in a browser with the url localhost:80/ExpressVis/home.