2020-04-19

今天的内容：

linux软件的安装
除说明外，本文引用内容均来自：微信公众号生信星球

记录下有意思的东西：

关于conda等更详细可以看这里

1. 安装miniconda

Miniconda 是一个 Anaconda 的轻量级替代，默认只包含了 python 和 conda，但是可以通过 pip 和 conda 来安装所需要的包。
清华的miniconda镜像地址

错误示范：

bio01@VM-0-10-ubuntu:~$ cd biosoft
bio01@VM-0-10-ubuntu:~/biosoft$ wget https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-py38_4.8.2-MacOSX-x86_64.sh  #下载

bio01@VM-0-10-ubuntu:~/biosoft$ ls
Miniconda3-py38_4.8.2-MacOSX-x86_64.sh

bio01@VM-0-10-ubuntu:~/biosoft$ bash Miniconda3-py38_4.8.2-MacOSX-x86_64.sh  #安装
Miniconda3-py38_4.8.2-MacOSX-x86_64.sh: line 405: /home/bio01/biosoft/:home/bio01/bashrc/conda.exe: cannot execute binary file: Exec format error    #此时我意识到下载错了版本

正解：

wget https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-py38_4.8.2-Linux-x86_64.sh
bash Miniconda3-py38_4.8.2-Linux-x86_64.sh
Thank you for installing Miniconda3!
bio01@VM-0-10-ubuntu:~$ source ~/.bashrc # 激活环境变量
(base) bio01@VM-0-10-ubuntu:~$ conda
(base) bio01@VM-0-10-ubuntu:~$ conda deactivate
bio01@VM-0-10-ubuntu:~$ 

conda后截图

2. 添加镜像

# 使用清华镜像
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
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
conda config --set show_channel_urls yes

3. 使用conda
   3.0 conda基本命令

positional arguments:
  command
    clean        Remove unused packages and caches.
    config       Modify configuration values in .condarc. This is modeled after the git config
                 command. Writes to the user .condarc file (/home/bio01/.condarc) by default.
    create       Create a new conda environment from a list of specified packages.
    help         Displays a list of available conda commands and their help strings.
    info         Display information about current conda install.
    init         Initialize conda for shell interaction. [Experimental]
    install      Installs a list of packages into a specified conda environment.
    list         List linked packages in a conda environment.
    package      Low-level conda package utility. (EXPERIMENTAL)
    remove       Remove a list of packages from a specified conda environment.
    uninstall    Alias for conda remove.
    run          Run an executable in a conda environment. [Experimental]
    search       Search for packages and display associated information. The input is a
                 MatchSpec, a query language for conda packages. See examples below.
    update       Updates conda packages to the latest compatible version.
    upgrade      Alias for conda update.

optional arguments:
  -h, --help     Show this help message and exit.
  -V, --version  Show the conda version number and exit.

 3.1 conda list 查看当前所有软件列表

bio01@VM-0-10-ubuntu:~$ conda list
# packages in environment at /home/bio01/miniconda3:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main    defaults
asn1crypto                1.3.0                    py38_0    defaults
ca-certificates           2020.1.1                      0    defaults
certifi                   2019.11.28               py38_0    defaults
cffi                      1.14.0           py38h2e261b9_0    defaults
chardet                   3.0.4                 py38_1003    defaults
conda                     4.8.2                    py38_0    defaults

 3.2 conda search搜索软件

bio01@VM-0-10-ubuntu:~$ conda search fastqc

图示fastqc部分版本
 3.3 conda install安装软件

conda install fastqc -y #自动安装最新版 可以去掉-y 手动
conda install fastqc=0.11.7 -y #选择版本号的安装

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

 3.4 conda remove fastqc -y卸载软件

Q： 请问不想用了怎么卸得畅快轻松？
A ：首先 rm -rf ~/miniconda3
B: 环境变量中去掉conda, vi ~/bash_profile 删除conda路径，退出保存
【有个小技巧：vim 中移动光标比如到第9行，使用dd就可以快速删除整行】
生信小白第三天

 3.5 conda enviroment

bio01@VM-0-10-ubuntu:~$ conda info --envs
# conda environments:
#
                         /home/bio01/biosoft/:/home/bio01/bashrc
base                  *  /home/bio01/miniconda3   #标*为默认环境
conda create -n rna-seq python=3 fastqc trimmomatic -y   #建立一个名叫rnaseq的conda环境，然后指定python版本是3，安装软件fastqc、trimmomatic（这两个可以一步完成）

bio01@VM-0-10-ubuntu:~$ conda info --envs   #查看环境
# conda environments:
#
                         /home/bio01/biosoft/:/home/bio01/bashrc
base                  *  /home/bio01/miniconda3
RNA-seq                  /home/bio01/miniconda3/envs/RNA-seq

bio01@VM-0-10-ubuntu:~$ conda activate RNA-seq   #因默认环境依然是miniconda3，故需要激活rna-seq的环境变量
(RNA-seq) bio01@VM-0-10-ubuntu:~$ conda info --envs
# conda environments:
#
                         /home/bio01/biosoft/:/home/bio01/bashrc
base                     /home/bio01/miniconda3
RNA-seq               *  /home/bio01/miniconda3/envs/RNA-seq
(RNA-seq) bio01@VM-0-10-ubuntu:~$ fastqc    #检测fastqc是否在这里，是否可用
Exception in thread "main" java.awt.HeadlessException: 
No X11 DISPLAY variable was set, but this program performed an operation which requires it.
    at java.desktop/java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:208)
    at java.desktop/java.awt.Window.<init>(Window.java:548)
    at java.desktop/java.awt.Frame.<init>(Frame.java:423)
    at java.desktop/java.awt.Frame.<init>(Frame.java:388)
    at java.desktop/javax.swing.JFrame.<init>(JFrame.java:180)
    at uk.ac.babraham.FastQC.FastQCApplication.<init>(FastQCApplication.java:63)
    at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:338)