Docker：部署数据科学栈Jupyter

持久化镜像存储

version: '3.3'
services:
    datascience-notebook:
        ports:
            - '57002:8888'
        container_name: jupyterR
        restart: always
        image: 'jupyter/datascience-notebook:r-4.1.3'
        command: start-notebook.sh --NotebookApp.token='***'

• mkdir -p ~/datascience && cd ~/datascience
• nano docker-compose.yml
• sudo docker-compose up -d
• sudo docker-compose logs
• sudo docker cp -a jupyterR:/opt /home/limour/upload/opt
• sudo docker cp -a jupyterR:/home/jovyan /home/limour/upload/home
• sudo docker-compose down && sudo docker volume prune

启动镜像

version: '3.3'
services:
    datascience-notebook:
        ports:
            - '57002:8888'
        container_name: jupyterR
        restart: always
        volumes:
            - '/home/limour/upload:/home/jovyan/upload'
            - '/home/limour/upload/opt/opt:/opt'
            - '/home/limour/upload/home/jovyan:/home/jovyan'
        image: 'jupyter/datascience-notebook:r-4.1.3'
        command: start-notebook.sh --NotebookApp.token='***'

• nano docker-compose.yml
• sudo chmod 777 -R /home/limour/upload/
• sudo docker-compose up -d
• sudo docker-compose logs
• NPS内网穿透加NPM面板反代

R包镜像

options(BioC_mirror="https://mirrors.ustc.edu.cn/bioc/") ##指定镜像，这个是中国科技大学镜像
options("repos" = c(CRAN="https://mirrors.tuna.tsinghua.edu.cn/CRAN/")) ##指定install.packages安装镜像，这个是清华镜像
options(ggrepel.max.overlaps = Inf)

• nano .Rprofile
• options()$repos ## 查看使用install.packages安装时的默认镜像
• options()$BioC_mirror ##查看使用bioconductor的默认镜像

conda镜像

Anaconda 镜像使用帮助；Docker安装A面板

• nano .condarc
• conda clean -i
• conda create -n seurat -c conda-forge r-seurat=4.1.1 -y
• conda activate seurat
• conda install -c conda-forge r-tidyverse -y
• conda install -c conda-forge r-irkernel -y
• Rscript -e "IRkernel::installspec(name='seurat', displayname='r-seurat')"
• wget -e "https_proxy=http://172.17.0.1:20171" https://github.com/chris-mcginnis-ucsf/DoubletFinder/archive/refs/heads/master.zip -O DoubletFinder-master.zip
• 上面的"https_proxy=http://172.17.0.1:20171"来自容器A面板