Centos 系列安装ArchR

Analyzing single-cell regulatory chromatin in R. • ArchRhttps://www.archrproject.com/

ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis

一、Installation of ArchR （Ideal）

ArchR is designed to be run on Unix-based operating systems such as macOS and linux. ArchR is NOT supported on Windows or other operating systems.

ArchR installation currently requires devtools and BiocManager for installation of GitHub and Bioconductor packages. Run the following commands to install the various dependencies used by ArchR:

# First, install devtools (for installing GitHub packages) if it isn’t already installed:
if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")

# Then, install BiocManager
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

# install ArchR:
devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories())

# Lastly, install all of the ArchR dependencies that arent installed by default:

library(ArchR)
ArchR::installExtraPackages()

二、Installation of ArchR（Reality）

理想是丰满的，现实很骨感。

2.1 解决依赖问题。

# dependencies
# install.packages(c("pkgdown", "roxygen2", "rversions", "urlchecker"))

# Warning
# Note:【libicui18n.so.58】: cannot open shared object file: No such file or directory
# ERROR: dependency ‘xml2’ is not available for package ‘pkgdown’
# 如果没有安装。
sudo yum install libicu-devel
sudo dnf install libicu-devel

# 进入R
remove.packages("xml2")

# 查看版本
sudo dnf install libicu60
ldconfig -p | grep icui18n
        libicui18n.so.67 (libc6,x86-64) => /lib64/libicui18n.so.67
        libicui18n.so.60 (libc6,x86-64) => /lib64/libicui18n.so.60
        libicui18n.so (libc6,x86-64) => /lib64/libicui18n.so

# 编译安装 或 软连接
sudo ln -s /lib64/libicui18n.so.60 /lib64/libicui18n.so.58
# or
sudo ln -s /usr/include/locale.h /usr/include/xlocale.h

wget https://github.com/unicode-org/icu/archive/release-58-3.tar.gz
tar xvzf release-58-3.tar.gz
cd icu-release-58-3/icu4c/source
./configure
make -j 16
make install

ls /usr/local/lib | grep libicu
#选择一个路径： 选择一个 R 默认搜索的路径，例如 /usr/lib64/R/lib。
sudo ln -s /usr/local/lib/libicui18n.so.58 /usr/lib64/R/lib/libicui18n.so.58
sudo ln -s /usr/local/lib/libicui18n.so.58 /lib64/libicui18n.so.58
# 或者修改bashrc
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib
source .bashrc

2.2 基本按照Github的流程安装，Seurat需要自己安装，具体步骤在我的另一篇博客。

# xml2 需要【libicui18n.so.58】
# 导致 "pkgdown", "roxygen2", "rversions", "urlchecker"没有安装成功
# 进入R
install.packages("xml2") 
install.packages(c("pkgdown", "roxygen2", "rversions", "urlchecker"))
if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

# 从官方的github下载，可能会报网络问题，多试几次，当前是1.0.2版本。
devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories())

# 另一种办法是
BiocManager::install("ArchR")

# 第三种选择是先下载，再安装
# /path/to 改为 你的实际路径
# https://api.github.com/repos/GreenleafLab/ArchR/tarball/master
library(devtools)
install_local("/path/to/GreenleafLab-ArchR-v1.0.2-8-gd9e741c.tar", repos = NULL, type = "source")


library(ArchR)
# Seurat未自动安装
ArchR::installExtraPackages()