# Docker：部署数据科学栈Jupyter

## 持久化镜像存储

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    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

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    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

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    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

生信 单细胞 开源 环境
Docker：部署数据科学栈Jupyter
https://occdn.limour.top/2378.html
Author
Limour
Posted on
October 2, 2022
Licensed under
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