infercnv hpc东南服务器 .libpath 最终使用monocle2环境安装

Young.Dr2023-11-01 10:43

安装不成功就用conda安装 conda install -c bioconda bioconductor-infercnv

Installing infercnv

There are several options for installing inferCNV. Choose whichever you prefer:

Option A: Install infercnv from BioConductor (preferred)

From within R, run the following:

复制代码

if (!requireNamespace("BiocManager", quietly = TRUE))
     install.packages("BiocManager")
BiocManager::install("infercnv")

Option B: Install infercnv from BioConductor devel (latest version)

From within R, run the following:

复制代码

if (!requireNamespace("BiocManager", quietly = TRUE))
     install.packages("BiocManager")
BiocManager::install(version = "devel")
BiocManager::install("infercnv")

BiocManager::install("plyranges")

Option C: Install infercnv from the Release tar.gz file

If installing using command line, download the latest release of InferCNV. Then use the following command on command line.

复制代码

R CMD install infercnv.tar.gz

Option D: Install infercnv from within R using devtools

If installing from directly within R, you can instead use the following command from within R.

conda install -c "conda-forge/label/gcc7" jags

复制代码

library("devtools")
devtools::install_github("broadinstitute/infercnv")

Option E: Install inferCNV by pulling the code using git followed by source installation:

Alternatively, you can pull the code from github and install it like so:

复制代码

git clone https://github.com/broadinstitute/infercnv
cd infercnv
R
> install.packages("./", repos=NULL, type="source")


.libPaths(c("/seu_share/home/chaojie/230218989/anaconda3/envs/r4.2.2/lib/R/library"))

其实不需要library，只要进入r4.2.2的环境就可以

library(infercnv) #https://github.com/broadinstitute/inferCNV/wiki
library(dplyr)
library(Seurat)
library(ggplot2)
library(parallelDist)
options(scipen = 100)
options(error = function() traceback(2))
Cstack_info()