HP DL580 G7 server system installation and deployment environment

Download centos7 image and make U disk boot disk

Download from Tsinghua mirroring

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

Set U disk as the first boot entry

F9 boot can enter the BIOS setup
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System environment to build

System version as follows:
CentOS Linux Release 7.7.1908 (Core)

Centos interface can not enter the system after the installation is complete, using the following command to the command line
ctrl alt F2 into the command line, enter a user name and password

• Open network, and set the automatic connection

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

• Installation R 3.6.1

yum install R

R installation of the package

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 installation error

jpeglib.h: No such file or directory

Installation system relies on the following

yum install -y libjpeg-devel

• Install perl modules

GD manually install modules, being given after installation

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

• Install gd dependent, you may still find some problems, consider installing cpan

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

• Finally, use cpan installation

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

• Installation module

参考module安装日志

• Installation and set up the source image conda

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

• Installation texlive

参考texlive安装日志

• Installation fastqc

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