Install the old version of seurat under Ubuntu
Demonstrate how to configure a single-cell data processing environment.
First prepare the Ubuntu system
Here is the first Huawei Cloud: https://www.huaweicloud.com/pricing.html#/ecs
It can be compared with other cloud services purchased on demand:
- https://www.amazonaws.cn/ec2/pricing/ec2-linux-pricing/ (Amazon China, aws)
- https://buy.cloud.tencent.com/price/cvm#tab0-list1 (Tencent cloud server)
- https://cn.aliyun.com/price/product#/ecs/detail (Alibaba Cloud server)
- https://cloud.google.com/compute/pricing?hl=zh-CN (Google Cloud Server)
- Others, Meituan Cloud, Baidu Cloud, etc. will not be shown one by one
Install R language
If the system R version is not enough, you need to upgrade
# First delete the old version of R that comes with the system
sudo apt-get--purge remove r-base r-base-core r-base-dev
sudo apt-get--purge remove r-base-core
sudo apt-get--purge remove r-base-dev
# sudo apt-get remove -y 'r-cran-*'
# apt-get remove will delete the software package and retain the software configuration file r
# apt-get purge will clear the software package and software configuration files at the same time
# Then update the Ubuntu source files
## Here, different Ubuntu systems are a bit different:
cat /etc/issue
# 18.04
# Use VIM to add the following code to/etc/apt/sources.list file
# deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
sudo apt-get update
sudo apt-get install -y r-base r-base-core r-base-dev
Install shiny-server and Rstudio-server
https://www.rstudio.com/products/shiny/shiny-server/
https://www.rstudio.com/products/rstudio/download-server/
sudo su - \
- c "R -e \"install.packages('shiny', repos='https://mirrors.tuna.tsinghua.edu.cn/CRAN/')\""
sudo apt-get install gdebi-core
wget https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.9.923-amd64.deb
sudo gdebi shiny-server-1.5.9.923-amd64.deb
wget https://download2.rstudio.org/server/trusty/amd64/rstudio-server-1.2.1335-amd64.deb
sudo gdebi rstudio-server-1.2.1335-amd64.deb
In this case, http://139.9.249.168:3838/ and http://139.9.249.168:8787 are accessible, but the designated ports need to be opened on Huawei Cloud.
Install the dependency package of the old version of seurat
How to know the dependency package of the old version of seurat? Run first:
packageurl <-"https://cran.r-project.org/src/contrib/Archive/Seurat/Seurat_2.3.4.tar.gz"
packageurl
install.packages(packageurl, repos=NULL, type="source")
Look at the error report and find the dependent package:
options()$repos
options()$BioC_mirror
options(BioC_mirror="https://mirrors.ustc.edu.cn/bioc/")options("repos"=c(CRAN="https://mirrors.tuna.tsinghua.edu.cn/CRAN/"))options()$repos
options()$BioC_mirror
# https://bioconductor.org/packages/release/bioc/html/GEOquery.html
if(!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
pkgs=c("ggplot2","cowplot","ROCR","mixtools","lars","ica","tsne","Rtsne","fpc","ape","pbapply","igraph","RANN","dplyr","RColorBrewer","irlba","reshape2","gplots","dtw","SDMTools","plotly","Hmisc","httr","tidyr","ggridges","metap","lmtest","fitdistrplus","png","doSNOW","reticulate","foreach","hdf5r","RcppEigen","RcppProgress")
BiocManager::install(pkgs,ask = F,update = F)
Dependent packages are not all smooth sailing, because the Ubuntu system lacks libraries:
sudo apt-get-y install libcurl4-gnutls-dev libxml2-dev libssl-dev subversion scons libfuse-dev gcc
sudo apt-get-y install libmariadb-client-lgpl-dev libcurl4-openssl-dev libudunits2-dev
After installing the necessary libraries, install the R package:
pkgs=c('curl','openssl','hdf5r','httr','plotly')
BiocManager::install(pkgs,ask = F,update = F)
About the failure of hdf5r
Google didn't find the answer. Looking at the log again, the library is also missing:
sudo apt-get install libhdf5-dev
Install hdf5r again to succeed.
pkgs='hdf5r'
BiocManager::install(pkgs,ask = F,update = F)
Finally successfully installed the old version of seurat
packageurl <-"https://cran.r-project.org/src/contrib/Archive/Seurat/Seurat_2.3.4.tar.gz"
packageurl
install.packages(packageurl, repos=NULL, type="source")
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