{"id":31581,"date":"2025-04-21T19:06:02","date_gmt":"2025-04-21T11:06:02","guid":{"rendered":"https:\/\/www.wsisp.com\/helps\/31581.html"},"modified":"2025-04-21T19:06:02","modified_gmt":"2025-04-21T11:06:02","slug":"%e5%a6%82%e4%bd%95%e5%9c%a8%e6%9c%8d%e5%8a%a1%e5%99%a8%e4%b8%ad%e4%bd%bf%e7%94%a8docker%e6%90%ad%e5%bb%barstudio%e5%88%86%e6%9e%90%e7%8e%af%e5%a2%83","status":"publish","type":"post","link":"https:\/\/www.wsisp.com\/helps\/31581.html","title":{"rendered":"\u5982\u4f55\u5728\u670d\u52a1\u5668\u4e2d\u4f7f\u7528docker\u642d\u5efaRstudio\u5206\u6790\u73af\u5883"},"content":{"rendered":"

\u5982\u4f55\u5728\u670d\u52a1\u5668\u4e2d\u4f7f\u7528docker\u642d\u5efaRstudio\u5206\u6790\u73af\u5883<\/h2>\n

\u9996\u5148\u786e\u4fdddocker\u5df2\u7ecf\u5b89\u88c5\u6210\u529f\u5e76\u4e14\u6210\u529f\u8fd0\u884c<\/h3>\n

# docker\u547d\u4ee4\u5728root\u6743\u9650\u4e0b\u8fd0\u884c，\u672c\u6559\u7a0b\u4ee5centos 9\u4e3a\u4f8b<\/span>
\n# \u67e5\u770bdocker\u8be6\u7ec6\u4fe1\u606f<\/span>
\ndocker<\/span> info<\/p>\n

\"image-20240905212426100\"<\/p>\n

\u6210\u529f\u5b89\u88c5\u5219\u4f1a\u663e\u793a\u5982\u56fe\u7684\u8be6\u7ec6docker\u4fe1\u606f<\/p>\n

# \u67e5\u770bdocker\u662f\u5426\u8fd0\u884c<\/span>
\nsystemctl status docker<\/span><\/p>\n

\"image-20240905213033177\"<\/p>\n

\u4e00\u3001\u4f7f\u7528dockerhub\u5df2\u6709\u955c\u50cf\u8fdb\u884c\u90e8\u7f72<\/h2>\n

1\u3001docker\u62c9\u53d6\u955c\u50cf<\/h3>\n

\u5728docker\u4e2d\u67e5\u627e\u6240\u9700\u7684docker\u955c\u50cfrstudio：\u6b64\u5904\u4ee5 rocker\/rstudio:latest\u4e3a\u4f8b<\/p>\n

docker<\/span> pull rocker\/rstudio:latest<\/p>\n

2\u3001\u4f7f\u7528\u4e0b\u8f7d\u597d\u7684\u955c\u50cf\u521b\u5efa\u5bb9\u5668<\/h3>\n

docker<\/span> run -itd<\/span> -p<\/span> 8888<\/span>:8787 -d<\/span> –restart<\/span> always –name<\/span> test<\/span> -v<\/span> \/home\/test\/rstudio\/:\/home\/test rocker\/rstudio:latest
\n# \u6ce8：\u4f7f\u7528\u62c9\u53d6\u5230\u670d\u52a1\u5668\u4e2d\u7684\u955c\u50cf\u5728test\u7528\u6237rstudio\u6587\u4ef6\u5939\u4e0b\u6302\u8f7d<\/span>
\n# 1\u3001\u5c3d\u91cf\u4e0d\u8981\u4f7f\u75288787\u7aef\u53e3，\u6539\u7528\u5176\u4ed6\u7aef\u53e3，\u59828888\u662f\u6211\u81ea\u5df1\u8bbe\u7f6e\u7684\u6620\u5c04\u7aef\u53e3<\/span>
\n# 2\u3001-d –restart always\u8bbe\u7f6e\u81ea\u52a8\u542f\u52a8\u5bb9\u5668，\u5426\u5219\u670d\u52a1\u5668\u91cd\u542f\u6216docker\u670d\u52a1\u91cd\u542f\u4e4b\u540e，\u8be5\u5bb9\u5668\u8fd8\u5904\u4e8estop\u72b6\u6001<\/span>
\n# 3\u3001\u82e5\u5fd8\u8bb0\u8bbe\u7f6erestart always\u53ef\u4f7f\u7528：docker update –restart=always test\u8fdb\u884c\u66f4\u65b0<\/span><\/p>\n

3\u3001\u5728\u521b\u5efa\u597d\u7684\u5bb9\u5668\u4e2d\u521b\u5efa\u7528\u6237<\/h3>\n

# \u8fdb\u5165test\u5bb9\u5668\u5185\u90e8<\/span>
\ndocker<\/span> exec<\/span> -it<\/span> test<\/span> bash<\/span><\/p>\n

# \u521b\u5efa\u7528\u6237：\u5373Rstudio-server\u767b\u5f55\u754c\u9762\u7684\u7528\u6237,\u6b64\u59041001\u4e3atest\u7528\u6237\u7684\u7528\u6237\u7ec4\u53f7，\u5177\u4f53\u6839\u636e\u81ea\u5df1\u7684\u5b50\u7528\u6237\u8fdb\u884c\u66f4\u6539<\/span>
\nadduser -u<\/span> 1001<\/span> test<\/span>
\n# \u8f93\u5165\u5bc6\u7801，\u91cd\u590d\u8f93\u5165\u4e24\u6b21\u5373\u53ef<\/span><\/p>\n

# \u66f4\u6539\u8be5\u5bb9\u5668\u4e2droot\u5bc6\u7801，\u8bbe\u7f6e\u5bc6\u7801\u5373\u53ef\u5728Rstudio\u7684\u7ec8\u7aef\u4e2d\u8fd0\u884csu\u547d\u4ee4\u8fdb\u5165root\u6743\u9650<\/span>
\npasswd<\/span><\/p>\n

4\u3001\u66f4\u6539\u7528\u6237rstudio\u6587\u4ef6\u5939\u6743\u9650<\/h3>\n

# \u7531\u4e8edocker\u521b\u5efa\u7684\u5bb9\u5668\u662f\u5728root\u6743\u9650\u4e0b\u8fdb\u884c\u7684，\u56e0\u6b64\u8be5\u6587\u4ef6\u5939\u6743\u9650\u5c5e\u4e8eroot，\u9700\u8981\u5c06\u5176\u6743\u9650\u6539\u4e3atest\u6240\u5c5e<\/span>
\nchown<\/span> -R<\/span> test.test \/home\/test\/rstudio<\/p>\n

5\u3001Rstudio-Server\u767b\u5f55<\/h3>\n

# \u67e5\u770b\u670d\u52a1\u5668ip<\/span>
\nhostname<\/span> -i<\/span>
\n#\u4f7f\u7528\u670d\u52a1\u5668ip+\u7aef\u53e3\u53f7\u5728\u6d4f\u89c8\u5668\u4e2d\u5373\u53ef\u767b\u5f55,\u8f93\u5165\u4e0a\u8ff0\u521b\u5efa\u7684\u8d26\u53f7\u5bc6\u7801<\/span>
\nip:8888<\/p>\n

\u81f3\u6b64，\u7528\u6237test\u5373\u53ef\u4f7f\u7528Finalshell\u8f6f\u4ef6\u8fde\u63a5\u670d\u52a1\u5668\u5728rstudio\u6587\u4ef6\u5939\u4e0b\u8fdb\u884c\u6587\u4ef6\u4e0a\u4f20\u548c\u4e0b\u8f7d，\u9700\u6ce8\u610f：\u7531\u4e8elinux\u5b89\u88c5R\u5305\u6240\u9700\u7684\u4f9d\u8d56\u5bfc\u81f4R\u5305\u5b89\u88c5\u4e0d\u4e0a，\u5728Rstudio\u7684\u7ec8\u7aef\u4e2dsu\u8fdb\u5165root\u6839\u636e\u76f8\u5e94\u7684R\u5305\u4f9d\u8d56\u5e93\u8fdb\u884c\u5b89\u88c5，\u968f\u540e\u5728\u5b89\u88c5R\u5305\u5373\u53ef\u5b89\u88c5\u6210\u529f<\/p>\n

\u4e8c\u3001\u81ea\u5b9a\u4e49Dockerfile\u8fdb\u884c\u90e8\u7f72\u2013\u63a8\u8350<\/h2>\n

\u7531\u4e8e\u4e0d\u540c\u7528\u6237\u5bf9R\u5305\u7684\u9700\u6c42\u4e0d\u4e00，\u56e0\u6b64\u63a8\u8350\u4f7f\u7528Dockerfile\u81ea\u5b9a\u4e49\u5b89\u88c5\u6240\u9700\u7684R\u5305，\u90e8\u7f72\u597d\u7684Rstudio-server\u5c06\u81ea\u5e26\u8fd9\u4e9bR\u5305，\u4e0d\u518d\u9700\u8981\u624b\u52a8\u5b89\u88c5<\/h3>\n

\u6b64\u5904\u4ecd\u4ee5\u4e0a\u8ff0\u7684\u7a7a\u767dR\u5305\u7684Rstudio-server\u4e3a\u4f8b<\/p>\n

1\u3001Dockerfile\u6587\u4ef6DIY<\/h3>\n

vim<\/span> Dockerfile
\n# \u6839\u636eR\u5305\u7684\u9700\u8981\u8fdb\u884c\u81ea\u5b9a\u4e49Dockerfile\u6587\u4ef6，\u4ee5\u4e0b\u5185\u5bb9\u590d\u5236\u5230Dockerfile\u6587\u4ef6\u4e2d<\/span>
\n# \u7531\u4e8eR\u5305\u5f88\u591a，\u56e0\u6b64\u82b1\u8d39\u65f6\u95f4\u8f83\u957f\u7ea63\u5c0f\u65f6，\u4e0d\u540c\u7528\u6237\u53ef\u4ee5\u81ea\u5b9a\u4e49\u6240\u9700\u7684R\u5305<\/span><\/p>\n

FROM rocker\/rstudio:latest <\/p>\n

ARG bioc_ver<\/span>=<\/span>3.19<\/span><\/p>\n

RUN apt-get<\/span> clean all &&<\/span> \\\\<\/span>
\n apt-get<\/span> update &&<\/span> \\\\<\/span>
\n apt-get<\/span> upgrade -y<\/span> &&<\/span> \\\\<\/span>
\n apt-get<\/span> install<\/span> -y<\/span> \\\\<\/span>
\n libhdf5-dev \\\\<\/span>
\n libssl-dev \\\\<\/span>
\n libxml2-dev \\\\<\/span>
\n libpng-dev \\\\<\/span>
\n libxt-dev \\\\<\/span>
\n zlib1g-dev \\\\<\/span>
\n libbz2-dev \\\\<\/span>
\n liblzma-dev \\\\<\/span>
\n libglpk40 \\\\<\/span>
\n libgit2-dev \\\\<\/span>
\n libbz2-dev \\\\<\/span>
\n libfontconfig1-dev \\\\<\/span>
\n libharfbuzz-dev \\\\<\/span>
\n libhdf5-dev \\\\<\/span>
\n patch \\\\<\/span>
\n libharfbuzz-dev \\\\<\/span>
\n libfribidi-dev \\\\<\/span>
\n libfreetype6-dev \\\\<\/span>
\n libpng-dev \\\\<\/span>
\n libtiff5-dev \\\\<\/span>
\n libjpeg-dev \\\\<\/span>
\n jags \\\\<\/span>
\n libgmp3-dev \\\\<\/span>
\n libmpfr-dev \\\\<\/span>
\n libv8-dev \\\\<\/span>
\n libcairo2-dev \\\\<\/span>
\n libmagick++-dev \\\\<\/span>
\n cmake \\\\<\/span>
\n libgdal-dev \\\\<\/span>
\n libssl-dev \\\\<\/span>
\n libssh2-1-dev \\\\<\/span>
\n libxml2-dev \\\\<\/span>
\n &&<\/span> apt-get<\/span> clean all &&<\/span> \\\\<\/span>
\n apt-get<\/span> purge &&<\/span> \\\\<\/span>
\n rm<\/span> -rf<\/span> \/var\/lib\/apt\/lists\/* \/tmp\/* \/var\/tmp\/*<\/p>\n

RUN Rscript -e<\/span> "install.packages(c('rmarkdown', 'tidyverse', 'workflowr', 'BiocManager', 'pacman', 'devtools', 'hdf5r', 'ggiraphExtra', 'magick','alphahull', 'dbscan'), ask = F, update = F, dependencies = T);"<\/span>
\nRUN Rscript -e<\/span> "BiocManager::install(version = '${bioc_ver}<\/span>')"<\/span>
\nRUN Rscript -e<\/span> "library(pacman);pacman::p_load(ggplot2, dplyr, data.table, magrittr, patchwork, RColorBrewer, clustree, cowplot,harmony, ggrepel, GSVA, clusterProfiler, survminer, ggpubr, stringr, rio, pheatmap, survival,sctransform, tibble,futile.logger, ggrisk, ggstatsplot, timeROC, maftools, edgeR, DESeq2, FactoMineR, factoextra, org.Hs.eg.db, stringi,cowplot, ggsci, VennDiagram, ggplotify, GEOquery, TCGAbiolinks, SummarizedExperiment, scCustomize, xml2, rvest, raster, rmarkdown, rticles, openai, update = F)"<\/span>
\nRUN Rscript -e<\/span> "BiocManager::install(c(\u2018seurat\u2019，'GSEABase', 'GEOquery', 'limma', 'impute', 'hgu133plus2.db', 'infercnv', 'SingleR', 'tidydr','simplifyEnrichment', 'biomaRt', 'EnsDb.Hsapiens.v86', 'Rhtslib', 'Rsamtools', 'GenomicAlignments','rtracklayer', 'GenomicFeatures', 'ensembldb', 'paletteer', 'ggdendro', 'monocle', 'BiocGenerics', 'DelayedArray', 'DelayedMatrixStats','S4Vectors','SingleCellExperiment','batchelor', 'kstreet13\/slingshot'), ask = F, update = F, dependencies = T)"<\/span><\/p>\n

2\u3001\u521b\u5efadocker\u955c\u50cf<\/h3>\n

docker<\/span> build -t<\/span> test_image\/rstudio:r.4.4.1 .<\/span>
\n#.\u8868\u793aDockerfile\u5728\u5f53\u524d\u76ee\u5f55\u4e0b<\/span><\/p>\n

3\u3001\u4f7f\u7528\u81ea\u5b9a\u4e49\u7684docker\u955c\u50cf\u521b\u5efa\u5bb9\u5668<\/h3>\n

docker<\/span> run -itd<\/span> -p<\/span> 8888<\/span>:8787 -d<\/span> –restart<\/span> always –name<\/span> test<\/span> -v<\/span> \/home\/test\/rstudio\/:\/home\/test test_image\/rstudio:r.4.4.1
\n# \u540e\u7eed\u64cd\u4f5c\u540c\u524d\u6587\u4e00\u6837，\u521b\u5efa\u7528\u6237，\u66f4\u6539rstudio\u6587\u4ef6\u5939\u6743\u9650<\/span><\/p>\n

4\u3001\u5728\u521b\u5efa\u597d\u7684\u5bb9\u5668\u4e2d\u521b\u5efa\u7528\u6237<\/h3>\n

# \u8fdb\u5165test\u5bb9\u5668\u5185\u90e8<\/span>
\ndocker<\/span> exec<\/span> -it<\/span> test<\/span> bash<\/span><\/p>\n

# \u521b\u5efa\u7528\u6237：\u5373Rstudio-server\u767b\u5f55\u754c\u9762\u7684\u7528\u6237,\u6b64\u59041001\u4e3atest\u7528\u6237\u7684\u7528\u6237\u7ec4\u53f7，\u5177\u4f53\u6839\u636e\u81ea\u5df1\u7684\u5b50\u7528\u6237\u8fdb\u884c\u66f4\u6539<\/span>
\nadduser -u<\/span> 1001<\/span> test<\/span>
\n# \u8f93\u5165\u5bc6\u7801，\u91cd\u590d\u8f93\u5165\u4e24\u6b21\u5373\u53ef<\/span><\/p>\n

# \u66f4\u6539\u8be5\u5bb9\u5668\u4e2droot\u5bc6\u7801，\u8bbe\u7f6e\u5bc6\u7801\u5373\u53ef\u5728Rstudio\u7684\u7ec8\u7aef\u4e2d\u8fd0\u884csu\u547d\u4ee4\u8fdb\u5165root\u6743\u9650<\/span>
\npasswd<\/span><\/p>\n

5\u3001\u66f4\u6539\u7528\u6237rstudio\u6587\u4ef6\u5939\u6743\u9650<\/h3>\n

# \u7531\u4e8edocker\u521b\u5efa\u7684\u5bb9\u5668\u662f\u5728root\u6743\u9650\u4e0b\u8fdb\u884c\u7684，\u56e0\u6b64\u8be5\u6587\u4ef6\u5939\u6743\u9650\u5c5e\u4e8eroot，\u9700\u8981\u5c06\u5176\u6743\u9650\u6539\u4e3atest\u6240\u5c5e<\/span>
\nchown<\/span> -R<\/span> test.test \/home\/test\/rstudio<\/p>\n

6\u3001Rstudio-Server\u767b\u5f55<\/h3>\n

# \u67e5\u770b\u670d\u52a1\u5668ip<\/span>
\nhostname<\/span> -i<\/span>
\n#\u4f7f\u7528\u670d\u52a1\u5668ip+\u7aef\u53e3\u53f7\u5728\u6d4f\u89c8\u5668\u4e2d\u5373\u53ef\u767b\u5f55,\u8f93\u5165\u4e0a\u8ff0\u521b\u5efa\u7684\u8d26\u53f7\u5bc6\u7801<\/span>
\nip:8888<\/p>\n

\u4e09\u3001\u5c06\u81ea\u5df1\u7684Dockerfile\u955c\u50cf\u6253\u5305\u8fc1\u79fb\u81f3\u65b0\u7684\u670d\u52a1\u5668\u8fdb\u884c\u90e8\u7f72<\/h2>\n

1\u3001\u5728\u539f\u670d\u52a1\u5668\u4e0a\u6253\u5305\u5df2\u6709\u955c\u50cf<\/h3>\n

# \u4ee5\u4e0a\u8ff0\u7684Dockfile\u521b\u5efa\u7684\u955c\u50cf\u4e3a\u4f8b<\/span>
\ndocker<\/span> save -o<\/span> test_image.tar test_image\/rstudio:r.4.4.1
\n# \u4f7f\u7528finalshell\u5c06\u5176\u4e0b\u8f7d\u5230\u672c\u5730，\u5e76\u4e0a\u4f20\u5230\u65b0\u670d\u52a1\u5668\u4e2d<\/span><\/p>\n

2\u3001\u5728\u65b0\u670d\u52a1\u5668\u4e0a\u90e8\u7f72\u955c\u50cf<\/h3>\n

docker<\/span> load -i<\/span> test_image.tar
\n# \u4f7f\u7528docker images\u67e5\u770b\u955c\u50cf，\u5373\u5728\u65b0\u670d\u52a1\u5668\u4e2d\u5b58\u5728test_image\/rstudio:r.4.4.1\u955c\u50cf<\/span><\/p>\n

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