4.2. Setup with Docker

Overview

As Docker is a convenient way to setup the software environment, we also provide an easier way to deploy SnpHub based on Docker.

To setup Snphub using Docker, you need to install Docker on your server first.

Also, samtools, along with bcftools, tabix and seqkit still need to be installed in order to pre-process your data.

Step.1

Clone (or download) project snphub4docker from GitHub.

git clone https://github.com/esctrionsit/snphub4docker

Step.2

Create Docker image of SnpHub.

cd snphub4docker
sudo ./snphub create image

Root permission is needed because of Docker.

Step.3

Pre-process your own re-seq data. (Or jump this step if just want to try on our sample data.)

Firstly, you need to fulfill the setup.conf.

vi ./setup.conf

Put the needed files into a folder, and fulfill setup_config.R with their name and folder path. An template data folder is provided at snphub4docker/Template_data.

Then, run command below to pre-process your data.

./snphub init -y

Step.4

Now, you can try SnpHub by creating a container (instance), binding your host port with it, and mount your own data (if there is).

sudo ./snphub create container -p 5123 -v /data/user_data

Options:

  • -p: Bind the host port with container. A random port will be bound when ignoring this parameter.
  • -v: Mount your own pre-processed re-seq data into container. SnpHub will run on a sample data when ignoring this parameter.

Step.5

Open your browser, and enjoy at http://localhost:5123.

(Port is the one that you choose at step.4 or a random value. Check more details using ./snphub list)

Parameters of the command: snphub

Program : snphub (Tools for visualizing re-seq data)
Version:  1.0.0
Updated on: Jun. 4th, 2020
Usage:    snphub <command> [options]
Commands:
  -- SnpHub on docker
     create      + to create a SnpHub Docker image or container
     list          to list all the containers created
     start         start a specific container
     stop          stop a specific container
     kill          kill (force stop) a specific container
     rm            delete a specific container
  -- SnpHub data pre-processing
     init          pre-processing the user provided re-seq data
Note: 
  Commands contain sub-commands are marked with "+" 
  Generally any operate on Docker needs root authority.
  We recommend to use root account when using commands related to Docker.
  Or using "sudo snphub <command> [options]".