Linux安装单细胞分析软件copykat

Linux安装单细胞分析软件copykat

测试环境

• Linux centos 7
• R 4.1.2
• minconda3
• 天意云24C192GB

安装步骤

新建环境

conda activate copykat
conda install r-base=4.1.2

安装基础软件

checkPkg <- function(pkg){
return(requireNamespace(pkg, quietly = TRUE))
}
if(!checkPkg("BiocManager")) install.packages("BiocManager")
if(!checkPkg("devtools")) install.packages("devtools")

安装依赖软件

library(devtools)
if(!checkPkg("RcppArmadillo")) install.packages("RcppArmadillo")
if(!checkPkg("RcppProgress")) install.packages("RcppProgress")
if(!checkPkg("markdown")) install.packages("markdown")
if(!checkPkg("R.utils")) install.packages("R.utils")
if(!checkPkg("NNLM")) install_github("linxihui/NNLM")
if(!checkPkg("copykat")) install_github("navinlabcode/copykat")
if(!checkPkg("Seurat")) BiocManager::install("Seurat")
if(!checkPkg("knitr")) BiocManager::install("knitr")
if(!checkPkg("GSVA")) BiocManager::install("GSVA")
if(!checkPkg("pheatmap")) BiocManager::install("pheatmap")
if(!checkPkg("ComplexHeatmap")) BiocManager::install("ComplexHeatmap")

安装copykat

install_github("Miaoyx323/stCancer")

报错与解决办法

XML报错引起连锁错误GSVA安装失败

解决方法：

conda install r-XML

httpuv报错引起seurat安装失败

ERROR: failed to lock directory ‘/home/zjw/miniconda3/envs/work/lib/R/library’ for modifying
Try removing ‘/home/zjw/miniconda3/envs/work/lib/R/library/00LOCK-httpuv’
ERROR: failed to lock directory ‘/home/zjw/miniconda3/envs/work/lib/R/library’ for modifying
Try removing ‘/home/zjw/miniconda3/envs/work/lib/R/library/00LOCK-RcppEigen’
ERROR: dependency ‘httpuv’ is not available for package ‘shiny’
* removing ‘/home/zjw/miniconda3/envs/work/lib/R/library/shiny’
  ERROR: dependency ‘shiny’ is not available for package ‘miniUI’
* removing ‘/home/zjw/miniconda3/envs/work/lib/R/library/miniUI’
  ERROR: dependencies ‘miniUI’, ‘shiny’, ‘RcppEigen’ are not available for package ‘Seurat’
* removing ‘/home/zjw/miniconda3/envs/work/lib/R/library/Seurat’

解决方法：

install.packages("httpuv",INSTALL_opts = '--no-lock')
conda install r-httpuv

RcppEigen报错

ERROR: failed to lock directory ‘/home/zjw/miniconda3/envs/work/lib/R/library’ for modifying
Try removing ‘/home/zjw/miniconda3/envs/work/lib/R/library/00LOCK-RcppEigen’

解决方法：

install.packages("RcppEigen",INSTALL_opts = '--no-lock')

conda install r-RcppEigen

hdf5r报错

Error in Read10X_h5("matrix.h5") :
  Please install hdf5r to read HDF5 files

解决方法：

sudo yum install hdf5-devel
install.packages("hdf5r")
conda install r-hdf5r

hdf5版本过低

configure: error: The version of hdf5 installed on your system is not sufficient. Please ensure that at least version 1.8.13 is installed
ERROR: configuration failed for package ‘hdf5r’

* removing ‘/home/zjw/miniconda3/envs/work/lib/R/library/hdf5r’

The downloaded source packages are in
        ‘/tmp/Rtmpr0m6Da/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("hdf5r") :
  installation of package ‘hdf5r’ had non-zero exit status

解决方法：

1. 下载hdf5-1.8.13的源码

wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.13/src/hdf5-1.8.13.tar.bz2

2. 编译安装

tar xjf hdf5-1.8.13.tar.bz2
cd hdf5-1.8.13
./configure --prefix=$HOME/.local/bin/hdf5-1.8.13
make && make install

3. 设置环境变量

export PATH=$HOME/.local/bin/hdf5-1.8.13/bin:$PATH
export LD_LIBRARY_PATH=$HOME/.local/bin/hdf5-1.8.13/lib:$LD_LIBRARY_PATH

4. 重新安装R包hdf5r

install.packages('hdf5r')

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