As Docker is a convenient way to setup the software environment, we also provide an easier way to deploy
SnpHub based on Docker.
Docker, you need to install
Docker on your server first.
samtools, along with
seqkit still need to be installed in order to pre-process your data.
Clone (or download) project
snphub4docker from GitHub.
git clone https://github.com/esctrionsit/snphub4docker
Docker image of
cd snphub4docker sudo ./snphub create image
Root permission is needed because of
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
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
Then, run command below to pre-process your data.
./snphub init -y
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
-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.
SnpHubwill run on a sample data when ignoring this parameter.
Open your browser, and enjoy at
(Port is the one that you choose at step.4 or a random value. Check more details using
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]".