惠普DL580 G7服务器系统安装与环境部署

下载centos7 镜像并制作U盘启动盘

从清华镜像源进行下载

wget https://mirrors.tuna.tsinghua.edu.cn/centos/7.7.1908/isos/x86_64/CentOS-7-x86_64-DVD-1908.iso

设置U盘为第一启动项

开机F9可以进入BIOS设置
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系统环境搭建

系统版本如下：
CentOS Linux release 7.7.1908 (Core)

安装完成后不能进入centos界面系统，使用如下命令进入命令行操作
ctrl alt F2 进入命令行，输入用户名和密码

• 打开网络，并设置自动连接

cd /etc/sysconfig/network-scripts
ifup ifcfg-enp4s0f2

• 安装R 3.6.1

yum install R

R包的安装

need_packages=c("reshape2","RColorBrewer","ggplot2","plyr","grid","Mfuzz","WGCNA","pheatmap")
install.packages(need_packages)

BGI need R package
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.10")
BiocManager::install("AnnotationDbi","EBSeq","NOISeq","DEGseq","clusterProfiler")
BiocManager::install("topGO")
BiocManager::install("Rgraphviz")
BiocManager::install(c("impute","preprocessCore")) #WGCNA

• DESeq2安装报错

jpeglib.h: No such file or directory

安装如下系统依赖

yum install -y libjpeg-devel

• perl 模块的安装

手动安装GD模块,安装完成后会报错

wget http://www.cpan.org/authors/id/L/LD/LDS/GD-1.16.tar.gz
cd GD-1.16
perl Makefile.PL
make
make install

• 安装gd依赖，发现可能还是存在一些问题，考虑使用cpan进行安装

yum install -y perl-GD
yum install -y gd-devel

• 最后使用cpan安装

cpan install YAML
cpan install Module:Build
cpan install Excel::Writer::XLSX

• 安装module

参考module安装日志

• conda 安装并设置镜像源

channels:
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
  - defaults
  - r
show_channel_urls: true

conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/

/home/yueyao/bio/tools/miniconda/4.5.1/bin/conda create -p /home/yueyao/bio/tools/snakemake/3.13.3 snakemake

• 安装texlive

参考texlive安装日志

• 安装fastqc

wget fastqc_v0.11.8.zip
unzip fastqc_v0.11.8.zip
mkdir -p /usr/local/Modules/modulefiles/fastqc/0.11.8