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 {{uploading-image-412605.png(uploading...)}}

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