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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.