NewMechine-Linux

## 1、基本信息查询
```shell
###查看基本信息

#查看系统版本
uname -a   #（Linux查看版本当前操作系统内核信息）
cat /proc/version #（Linux查看当前操作系统版本信息）
cat /etc/issue; cat /etc/redhat-release #（Linux查看版本当前操作系统发行版信息）

# memory内存
free -h

# 查看磁盘及分区情况
df -Th
lsblk
fdisk -lgg
```

## 2、检查是否安装好gcc（未安装，其他很多软件会安装不了）
```shell
gcc -v
#如果未安装
yum install gcc #即可安装
```

## 3、安装python（系统默认安装了python2，可以which python）
```shell
wget https://www.python.org/ftp/python/3.8.0/Python-3.8.0.tgz
tar xvzf Python-3.8.0.tgz
cd Python-3.8.0
mkdir -p /usr/local/python3
./configure --prefix=/usr/local/python3
make && make install
ln -s /usr/local/python3/python3.8 /usr/local/bin/python3
ln -s /usr/local/python3/pip3 /usr/local/bin/pip3
```

## 4、优先安装系统一些软件和依赖包
附：centOS7的一些依赖包
yum -y install librsvg2-devel.x86_64 poppler-devel.x86_64 poppler-glib.x86_6 fftwdevel avahi-compat-libdns_sd-devel mesa-libGL-devel glew-devel ftgl-devel e2fsprogs-devel uuid uuid-devel libuuid-devel libffi-devel patch ncurses-devel openssl-devel libcurl-devel gnutls-devel libtasn1-devel p11-kit-devel gmp-devel nettle-devel libbz2-devel liblzma-devel python-sphinx.noarch libdb-devel gsl.x86_64 gsl-devel.x86_64 valgrind.x86_64 valgrind-devel.x86_64 tcl-devel.x86_64 tcl.x86_64 tk.x86_64 tk-devel.x86_64 gsl.x86_64 gsl-devel.x86_64 ocaml.x86_64 ocaml-compiler-libs.x86_64 ocaml-curses-devel.x86_64 sqlite-devel lzo-devel lzo cyrus-sasl-devel lftp screen patch ncurses-devel openssl-devel libcurl-devel gnutls-devel libtasn1-devel p11-kit-devel gmp-devel nettle-devel libbz2-devel liblzma-devel libxml2-devel.x86_64 ghostscript.x86_64 graphviz-devel.x86_64 graphviz.x86_64 gd.x86_64 gd-devel.x86_64 ImageMagick.x86_64 glibc-headers gcc-c++ gcc-gfortran libcurl-devel.x86_64 ncurses-devel.x86_64 libxml2-devel.x86_64 xz-devel.x86_64 tree nginx readline-devel libXt-devel bzip2-devel cairo-devel.x86_64 lapack lapack-devel.x86_64 pcre-devel.x86_64 graphvizdevel.x86_64 libpng-devel.x86_64 openssl-devel.x86_64 git perl-App-cpanminus.noarch perl-CPAN.noarch build-essential rpcbind nfs-uitls gd.x86_64 libtiff-devel.x86_64 gnuplot.x86_64 lftp.x86_64 mariadb-devel mariadb.x86_64 mono-devel mesa-libGLU-devel.x86_64 freeglut-devel.x86_64 pixman-devel.x86_64 xorg-x11-server-Xvfb.x86_64 blas64-devel.x86_64 blas64.x86_64 lapack64-devel.x86_64 lapack64.x86_64 atlas-devel.x86_64 atlas.x86_6 freetype-devel
yum install bzip2

## 5、安装java
```
## download from https://www.oracle.com/technetwork/java/javase/downloads/jdk13-downloads-5672538.html
mkdir /usr/java
mv jdk-13.0.1_linux-x64_bin.tar.gz /usr/java
cd /usr/java
tar xvzf jdk-13.0.1_linux-x64_bin.tar.gz
cd jdk-13.0.1
vim /etc/profile #最后一行追加输入内容： PATH=$PATH:/usr/local/samtools/bin:/usr/java/jdk-13.0.1/bin
source /etc/profile
java -version # test
```

## 6、安装python包（通过pip安装）
```
## 永久使用国内pypi镜像安装
mkdir ~/.pip; vi ~/.pip/pip.conf  #随后输入下面内容
[global] 
index-url = https://pypi.tuna.tsinghua.edu.cn/simple
[install]
trusted-host = https://pypi.tuna.tsinghua.edu.cn  # trusted-host 此参数是为了避免麻烦，否则使用的时候可能会提示不受信任

### 国内源说明
清华大学：https://pypi.tuna.tsinghua.edu.cn/simple
阿里云：http://mirrors.aliyun.com/pypi/simple/
豆瓣：http://pypi.douban.com/simple/
```
```
### 安装python包
pip3 install numpy #轻松安装
### 经过第4步安装一些依赖包后，下面报错比较少
pip3 install matplotlib #include <ft2build.h> \n error: command 'gcc' failed with exit status 1
#需要环境中安装好 freetype-devel和libpng-devel
yum install libpng-devel freetype-devel
#仍然报错gcc: error trying to exec 'cc1plus': execvp: No such file or directory\n  error: command 'gcc' failed with exit status 1
yum install gcc-c++
#successfully

## 安装readline包，让命令行可以使用删除键
pip3 install readline
```

## 7、perl安装
```
wget https://www.cpan.org/src/5.0/perl-5.30.0.tar.gz
tar xvzf perl-5.30.0.tar.gz
./Configure -Dprefix=/usr/local/perl-5.30 -Dusethreads -Uversiononly
make && make install
perl -v
```

## 8、R语言安装
```
## download from https://cran.r-project.org/src/base/R-3/ 
tar xvzf R-3.6.1.tar.gz
cd R-3.6.1
mkdir -p /usr/local/R-3.6
./configure --prefix=/usr/local/R-3.6
make && make install
vim /etc/profile #最后一行追加输入内容： PATH=$PATH:/usr/local/samtools/bin:/usr/local/R-3.6/bin
# 进入R，安装包ggplot2 ggpubr karyoploteR
install.packages("ggplot2")
install.packages("ggpubr")
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("karyoploteR")
```

## 9、docker安装
```
yum install docker-io #安装
service docker start #启动服务
docker images #查看镜像
#配置文件/etc/docker/daemon.json的内容如下：
{
    "registry-mirrors": ["https://docker.mirrors.ustc.edu.cn","https://hub-mirror.c.163.com"],
    "insecure-registries": ["docker.reg.me:6698"],
    "max-concurrent-downloads": 20,
    "live-restore": true,
    "max-concurrent-uploads": 10,
    "debug": true,
    "data-root": "/home/hadoop/software/docker/data",
    "exec-root": "/home/hadoop/software/docker/exec",
    "log-opts": {
      "max-size": "100m",
      "max-file": "5"
    }
}
#注意需要修改 data-root和exec-root的目录，或者删除这两个属性。
#通过docker pull 从镜像仓库中拉取或者更新指定镜像，如：
docker pull docker.reg.me:6698/dna_job/call_variant:1.0
```

**报错1**：无主机（需要配置host）

![](/media/202211/2022-11-10_165825&2oe58BFGKamik70UcrLW.png)

配置/etc/hosts文件，添加行内容
192.168.1.28 docker.reg.me

**报错2**：

![](/media/202211/2022-11-10_165850&biQOjGJZlKWdq1NBAU8s.png)

继续配置：
`systemctl daemon-reload && systemctl enable docker && systemctl restart docker`
配置时报错，通过提示的“systemctl status docker.service”查看具体信息：

![](/media/202211/2022-11-10_165923&M7wbL2XFeuEKAgYvCZPB.png)

可以看到，需要更改/etc/docker/daemon.json内容，后面如此反复配置，查看具体错误信息后，最终配置为内容：
```
{
    "registry-mirrors": ["https://docker.mirrors.ustc.edu.cn","https://hub-mirror.c.163.com"],
    "insecure-registries": ["docker.reg.me:6698"],
    "max-concurrent-downloads": 20,
    "live-restore": true,
    "max-concurrent-uploads": 10,
    "debug": true
}
```
**注意最后一个参数不能有“,”**

**用户使用权限**
配置完后可以用了，但是其他非root用户使用不了，报错：`Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Get http://%2Fvar%2Frun%2Fdocker.sock/v1.26/images/json: dial unix /var/run/docker.sock: connect: permission denied`
```
### 新建docker用户组
sudo groupadd docker
sudo usermod -aG docker lvlaihui
systemctl restart docker
```
**用户使用报错：**
通过uname -r 查看到是“3.10.0-514.el7.x86_64”版本。需要使用yum update进行系统和内核升级。

## 10、安装bwa、samtools
```
#bwa  #download from https://sourceforge.net/projects/bio-bwa/files/bwa-0.7.17.tar.bz2/download
tar xvjf bwa-0.7.17.tar.bz2
cd bwa-0.7.17
make
cp bwa /usr/local/bin/
# samtools   #download from https://sourceforge.net/projects/samtools/files/samtools/1.9/
tar xvjf samtools-1.9.tar.bz2
cd samtools-1.9
mkdir -p /usr/local/samtools
./configure --prefix=/usr/local/samtools
make && make install
vim /etc/profile #最后一行追加输入内容： PATH=$PATH:/usr/local/samtools/bin
```