To make good use of the old, broken device… I decided to set up a server to accumulate experience. Considering the portability of the things I will be setting up, using Docker in containers is convenient for migration and usage.

Installation

The environment system uses Manjaro, since this is what I am most familiar with. And ArchWiki can provide help for many strange problems. Installing Docker is very simple:

sudo pacman -S docker
# To allow ordinary users to use Docker, you need to add the corresponding user group and add the user to the group.
sudo groupadd docker
sudo gpasswd -a ${USER} docker
# Alternatively, you can use the `usermod` command:
sudo usermod -Ga docker ${USER}
# If it has already been enabled, restart it; no need to enable it again.
systemctl start docker
systemctl enable docker

To speed up image (images) downloads, set up a domestic mirror source (registry mirror) for Docker Hub. The configuration file is /etc/docker/daemon.json. After configuring, execute sudo systemctl restart docker:

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{
  "registry-mirrors": ["https://docker.mirrors.ustc.edu.cn/"]
}

Image Creation and Internal Operations

Prepare to install R and the sscClust package in a container. The company’s server is CentOS6, so pull the corresponding image:

1	docker pull centos:6

However, after pulling the above image, it could not start normally. According to here, this might be an issue with the official image. So I switched to pulling centos:7, which worked fine after changing versions.

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docker run -dti IMAGE_ID /bin/bash
# Log in to Docker for operations. Note that when logged in, you are root; operate carefully...
docker exec -it CONTAINER_ID /bin/bash

After logging in, install vim and set up basic environment variables. Then start installing R.

yum -y install epel-release
# Change the image source
yum install wget
mv /etc/yum.repos.d/CentOS-Base.repo /etc/yum.repos.d/CentOS-Base.repo.bak
mv /etc/yum.repos.d/epel.repo /etc/yum.repos.d/epel.repo.bak
wget -O /etc/yum.repos.d/CentOS-Base.repo http://mirrors.aliyun.com/repo/Centos-7.repo
wget -O /etc/yum.repos.d/epel.repo http://mirrors.aliyun.com/repo/epel-7.repo
# Different image sources have different package versions, delete existing cache to prevent errors.
yum clean all
yum -y makecache
yum -y install R

Install some system software packages required for R package installation.

1	yum install -y openssl-devel libcurl-devel libxml2-devel gsl-devel

After entering R, start installing sscClust (installing R will automatically install a lot of dependencies; installing this package will have even more dependencies…)

options("repos" = c(CRAN="https://mirrors.ustc.edu.cn/CRAN/"))
options(BioC_mirror="http://mirrors.ustc.edu.cn/bioc/")
source("http://bioconductor.org/biocLite.R")
install.packages("devtools")
biocLite(c('SingleCellExperiment', 'scran', 'SC3', 'zinbwave', 'BiocParallel'))
devtools::install_github("Japrin/sscClust")

If there are no special network issues, sscClust should install smoothly. Finally, save the changes made to the Docker container as an image. After saving, it will display a series of sha256 values. Use docker images to see the saved images.

1	docker commit CONTAINER_ID r/sscclust

Docker Usage Record

Installation

Image Creation and Internal Operations