一般来说,新安装的ubuntu系统都太干净,缺很多库文件,下面的代码先运行一波!
<pre data-tool="mdnice编辑器" style="margin: 10px 0px; padding: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; color: rgb(0, 0, 0); font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration-style: initial; text-decoration-color: initial; border-radius: 5px; box-shadow: rgba(0, 0, 0, 0.55) 0px 2px 10px;">`sudo apt install --fix-missing libcurl4-openssl-dev libxml2-dev libgdal-dev libssl-dev libglu1-mesa-dev libmagick++-dev libudunits2-dev
sudo apt install -y libcurl4-gnutls-dev
sudo apt install -y libxml2-dev
sudo apt install -y openssl
sudo apt install -y libssl-dev` </pre>
安装最新版R语言
使用root权限(系统管理员)安装最新版的R,我们的ubuntu是20,所以选择focal这个代号,然后是cran40,全部的代码如下:
<pre data-tool="mdnice编辑器" style="margin: 10px 0px; padding: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; color: rgb(0, 0, 0); font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration-style: initial; text-decoration-color: initial; border-radius: 5px; box-shadow: rgba(0, 0, 0, 0.55) 0px 2px 10px;">sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 sudo add-apt-repository 'deb https://mirrors.ustc.edu.cn/CRAN/bin/linux/ubuntu focal-cran40/' sudo apt update sudo apt install r-base
</pre>
实际上还需要使用root权限(系统管理员)安装一些R包。
安装一些R包
这里我们使用root权限(系统管理员):sudo R
<pre data-tool="mdnice编辑器" style="margin: 10px 0px; padding: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; color: rgb(0, 0, 0); font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration-style: initial; text-decoration-color: initial; border-radius: 5px; box-shadow: rgba(0, 0, 0, 0.55) 0px 2px 10px;">`options()BioC_mirror
options(BioC_mirror="https://mirrors.ustc.edu.cn/bioc/")
options(BioC_mirror="http://mirrors.tuna.tsinghua.edu.cn/bioconductor/")
options("repos" = c(CRAN="https://mirrors.tuna.tsinghua.edu.cn/CRAN/"))
options()BioC_mirror
https://bioconductor.org/packages/release/bioc/html/GEOquery.html
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("KEGG.db",ask = F,update = F)` </pre>
一般来说不会报错,然后继续安装更多的包:
<pre data-tool="mdnice编辑器" style="margin: 10px 0px; padding: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; color: rgb(0, 0, 0); font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration-style: initial; text-decoration-color: initial; border-radius: 5px; box-shadow: rgba(0, 0, 0, 0.55) 0px 2px 10px;">`BiocManager::install(c("GSEABase","GSVA","clusterProfiler" ),ask = F,update = F)
BiocManager::install(c("GEOquery","limma","impute" ),ask = F,update = F)
BiocManager::install(c("org.Hs.eg.db","hgu133plus2.db" ),ask = F,update = F)
options()$repos
install.packages('WGCNA')
install.packages(c("FactoMineR", "factoextra"))
install.packages(c("ggplot2", "pheatmap","ggpubr"))
library("FactoMineR")
library("factoextra")
library(GSEABase)
library(GSVA)
library(clusterProfiler)
library(ggplot2)
library(ggpubr)
library(hgu133plus2.db)
library(limma)
library(org.Hs.eg.db)
library(pheatmap)
BiocManager::install("ChAMP")` </pre>
不得不说,有一些R包真的很难安装,搞了一个下午,比如ChAMP这个甲基化芯片数据处理包,如下;
图片我的空白ubuntu系统,全部运行完上述代码后,有327个包:
<pre data-tool="mdnice编辑器" style="margin: 10px 0px; padding: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; color: rgb(0, 0, 0); font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration-style: initial; text-decoration-color: initial; border-radius: 5px; box-shadow: rgba(0, 0, 0, 0.55) 0px 2px 10px;">(base) jmzeng@biotrainee:/usr/local/lib/R/site-library$ du -h -d 1 |tail 404K ./ruv 3.2M ./biovizBase 4.5M ./colorspace 1.8M ./prettydoc 444K ./lazyeval 392K ./statmod 5.2M ./WGCNA 156K ./generics 8.0M ./urltools 2.9G .
</pre>
配置网络服务(选修)
<pre data-tool="mdnice编辑器" style="margin: 10px 0px; padding: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; color: rgb(0, 0, 0); font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration-style: initial; text-decoration-color: initial; border-radius: 5px; box-shadow: rgba(0, 0, 0, 0.55) 0px 2px 10px;">sudo apt install -y nginx curl
</pre>
同时需要设置好 /var/www/html 文件夹权限,就是需要增加一个 www-data 的用户组,里面包含的用户都是可以访问的。
<pre data-tool="mdnice编辑器" style="margin: 10px 0px; padding: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; color: rgb(0, 0, 0); font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration-style: initial; text-decoration-color: initial; border-radius: 5px; box-shadow: rgba(0, 0, 0, 0.55) 0px 2px 10px;">`sudo chgrp -R www-data /var/www
sudo usermod -a -G www-data jmzeng
sudo usermod -a -G www-data ubuntu
sudo chmod -R 2770 /var/www/html` </pre>
同时,也需要管理ubuntu的端口,Nginx安装后,理论上IP可以在浏览器打开访问,但是要求网页端口80的开通的。
ufw是一个主机端的iptables类防火墙配置工具
<pre data-tool="mdnice编辑器" style="margin: 10px 0px; padding: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; color: rgb(0, 0, 0); font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration-style: initial; text-decoration-color: initial; border-radius: 5px; box-shadow: rgba(0, 0, 0, 0.55) 0px 2px 10px;">sudo ufw enable # 打开防火墙 sudo ufw allow 80 ## 打开端口 sudo ufw status ### 查看防火墙状态 sudo ufw allow 8787 ## 打开端口
</pre>
服务器那边打开端口才可以。
安装rstudio-server
参考:https://rstudio.com/products/rstudio/download-server/debian-ubuntu/
一定要看清楚ubuntu系统的版本哦!
<pre data-tool="mdnice编辑器" style="margin: 10px 0px; padding: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; color: rgb(0, 0, 0); font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration-style: initial; text-decoration-color: initial; border-radius: 5px; box-shadow: rgba(0, 0, 0, 0.55) 0px 2px 10px;">sudo apt-get install gdebi-core wget https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.3.1056-amd64.deb sudo gdebi rstudio-server-1.3.1056-amd64.deb
</pre>
在这个版本上面,我浪费了至少两个小时。安装shiny和rsutdio的服务器,官网找到最新版咯
- https://www.rstudio.com/products/rstudio/download-server/
- https://www.rstudio.com/products/shiny/shiny-server/
自己寻找地址啦!
配置shiny权限(选修)
这个呢,基本上只有你真正需要开发自己的网页工具,才用得上哈!
<pre data-tool="mdnice编辑器" style="margin: 10px 0px; padding: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; color: rgb(0, 0, 0); font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration-style: initial; text-decoration-color: initial; border-radius: 5px; box-shadow: rgba(0, 0, 0, 0.55) 0px 2px 10px;">sudo systemctl restart shiny-server
</pre>
可能需要经常重启,安装成功之后查看端口开放情况:netstat -tln
配置用户组:
<pre data-tool="mdnice编辑器" style="margin: 10px 0px; padding: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; color: rgb(0, 0, 0); font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration-style: initial; text-decoration-color: initial; border-radius: 5px; box-shadow: rgba(0, 0, 0, 0.55) 0px 2px 10px;">sudo groupadd shiny sudo chgrp -R shiny /srv/shiny-server/ sudo usermod -a -G shiny jmzeng
</pre>
一些自己开发的网页小工具,可以统一存放在 /srv/shiny-server/ 目录。
<pre data-tool="mdnice编辑器" style="margin: 10px 0px; padding: 0px; max-width: 100%; box-sizing: border-box !important; overflow-wrap: break-word !important; color: rgb(0, 0, 0); font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration-style: initial; text-decoration-color: initial; border-radius: 5px; box-shadow: rgba(0, 0, 0, 0.55) 0px 2px 10px;">`sudo chmod -R 2775 /srv/shiny-server/
cd /srv/shiny-server/
mkdir -p plot123
cd plot123
mkdir lineplot dotplot scatterplot boxplot barplot histplot pieplot density
mkdir violinplot qqplot errorplot
mkdir veen upsetr heatmap circos volcano
mkdir genestructure
cd /srv/shiny-server/
mkdir analysis
cd analysis
mkdir deg det deu enrich gsea gsva wgcna timeseries pca tsne
mkdir kmsurvival cox forest
cd /srv/shiny-server/
mkdir database
cd database
mkdir tcga icgc ccle gtex encode roadmap
mkdir ncbi ucsc ensembl
cd /srv/shiny-server/
mkdir paper
cd paper `</pre>
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