安装代谢组学流程开发所需的软件

安装R 3.6.1

sudo apt install r-base

R x11可以使用了

sudo apt-get install libcairo2

进入R3.6.1目录

./configure --with-cairo
make
sudo make install
#cairo
apt-get install libcairo2-dev
apt-get install libxt-dev
#进入R
install.packages('Cairo')

安装软件

安装xcms

#在R 3.6.1中，安装xcms包
if (!requireNamespace("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("xcms")
#提示没有ncdf4包安装
#安装ncdf4包
#下载网址http://cirrus.ucsd.edu/~pierce/ncdf/
wget -c http://cirrus.ucsd.edu/~pierce/ncdf/ncdf4_1.13.tar.gz
#R CMD INSTALL ncdf4_1.13.tar.gz 
#提示没有nc-config
#安装nc-config
sudo apt-get install libnetcdf-dev
R CMD INSTALL ncdf4_1.13.tar.gz 
#报错，提示没有XML包
Warning messages:
1: In install.packages(...) :
 installation of package ‘XML’ had non-zero exit status
2: In install.packages(...) :
 installation of package ‘mzID’ had non-zero exit status
3: In install.packages(...) :
 installation of package ‘MSnbase’ had non-zero exit status
4: In install.packages(...) :
 installation of package ‘xcms’ had non-zero exit status
#退出R运行命令
sudo apt-get install libxml2-dev
#再进入R安装xcms
#测试是否安装成功
> library(xcms)

安装CAMERA

if (!requireNamespace("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("CAMERA")
library(CAMERA)

安装corrplot

install.packages("corrplot")
library(corrplot)

安装ggord

install.packages('devtools')
#报错，提示没有openssl包
Warning messages:
1: In install.packages("devtools") :
  installation of package ‘openssl’ had non-zero exit status
2: In install.packages("devtools") :
  installation of package ‘httr’ had non-zero exit status
3: In install.packages("devtools") :
  installation of package ‘gh’ had non-zero exit status
4: In install.packages("devtools") :
  installation of package ‘covr’ had non-zero exit status
5: In install.packages("devtools") :
  installation of package ‘usethis’ had non-zero exit status
6: In install.packages("devtools") :
  installation of package ‘devtools’ had non-zero exit status
#安装ssl
sudo apt-get install libssl-dev
#重新安装devtools

library(devtools)
install_github('fawda123/ggord')
#报错
Downloading GitHub repo fawda123/ggord@HEAD
Error in utils::download.file(url, path, method = method, quiet = quiet,  :
download from 'https://api.github.com/repos/fawda123/ggord/tarball/HEAD' failed
#解决办法
#下载安装包fawda123-ggord-v1.1.5-1-g6faffc5.tar.gz
wget -c https://api.github.com/repos/fawda123/ggord/tarball/HEAD
#进入R，运行
install.packages("fawda123-ggord-v1.1.5-1-g6faffc5.tar.gz")
#还可以通过Y叔的install_zip_gh()函数安装，参考此文
Y叔的文章[听说你装不了github的包](https://mp.weixin.qq.com/s?__biz=MzI5NjUyNzkxMg==&mid=2247489732&idx=1&sn=e80e8ecc6d1c9259c402d3c7f088ffbd&chksm=ec43a983db3420951bff0e1d5fd2102b8724cdb1b0749a7599eb27dcdf77b47d6515084a1944&scene=126&sessionid=1598595400&key=5deef5cfd85208d391fbd55c3561c0a55549d0b5673c99130cb0d9948b05b05d3740719d863a7625ba388f52675fb01d12babdb6efc59a42b62c785e2700833f2f46784badc79eb2eeaaeeb83cbc3d98f9f4ba2d35136ada32453b72cc7b4c91f6a11547ae1417f8548e1056cf8e4c520df348ec5d213108eed891cbcef8be09&ascene=1&uin=MTAyNzc5MDEyMQ%3D%3D&devicetype=Windows+10+x64&version=62090529&lang=zh_CN&exportkey=AbZoV4R84DXgVow78pm3Ew4%3D&pass_ticket=vkePZHK4GSKJTe0vz6HEf2jB3IbvID%2BzCztW0Kd90lfRNoYfVlJ%2BoGxfLOmGQvSs)

#提示没有ggrepel包
install.packages("ggrepel")
#再安装ggord
#测试
library(ggord)

安装pheatmap

library(devtools)
install_github("raivokolde/pheatmap")

安装mixOmics

if (!requireNamespace("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("mixOmics")
library(mixOmics)

ProteoWizard：https://hub.docker.com/r/chambm/pwiz-skyline-i-agree-to-the-vendor-licenses

docker pull chambm/pwiz-skyline-i-agree-to-the-vendor-licenses

添加普通用户docker权限

sudo groupadd docker     #添加docker用户组
sudo gpasswd -a $USER docker     #将登陆用户加入到docker用户组中
newgrp docker     #更新用户组
docker ps    #测试docker命令是否可以使用sudo正常使用