先上今天的思维导图：

linux如何安装软件.png

1. 了解conda

简单的说——linux的应用商店，除此之外还有几个概念。

bioconda
miniconda
conda
anaconda
以上四者区别，参考关于bioconda, miniconda, conda, anaconda的区别

来源：生信星球

2. 安装miniconda

（1）进入网站
搜索“miniconda 清华”，进入。搜素得到链接为：https://mirror.tuna.tsinghua.edu.cn/help/anaconda/

进入页面如上

（2）查看服务器
登录输入命令 uname -a

bio18@VM-0-10-ubuntu:~$ uname -a
Linux VM-0-10-ubuntu 4.15.0-54-generic #58-Ubuntu SMP Mon Jun 24 10:55:24 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

（3）安装最新版
进入（1）中页面，https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/
找到下载最新版，复制链接
在linux中，Windows复制——鼠标左键点一下，粘贴——右键；Mac直接cmd + c 复制，cmd + v 粘贴

进入到biosoft目录，安装 cd biosoft
复制链接 wget 刚刚复制的链接

bio18@VM-0-10-ubuntu:~/biosoft$ wget https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-latest-Linux-x86_64.sh
--2020-04-08 20:52:33--  https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-latest-Linux-x86_64.sh
Resolving mirrors.tuna.tsinghua.edu.cn (mirrors.tuna.tsinghua.edu.cn)... 101.6.8.193, 2402:f000:1:408:8100::1
Connecting to mirrors.tuna.tsinghua.edu.cn (mirrors.tuna.tsinghua.edu.cn)|101.6.8.193|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 85055499 (81M) [application/octet-stream]
Saving to: ‘Miniconda3-latest-Linux-x86_64.sh’

Miniconda3-latest-L 100%[===================>]  81.12M  3.52MB/s    in 21s

2020-04-08 20:52:55 (3.84 MB/s) - ‘Miniconda3-latest-Linux-x86_64.sh’ saved [85055499/85055499]

bio18@VM-0-10-ubuntu:~/biosoft$ bash Miniconda3-latest-Linux-x86_64.sh

Welcome to Miniconda3 4.8.2

In order to continue the installation process, please review the license
agreement.
Please, press ENTER to continue
>>>
===================================

根据提示完成安装
（4）激活conda
输入命令 source ~/.bashrc

Thank you for installing Miniconda3!
bio18@VM-0-10-ubuntu:~/biosoft$ source ~/.bashrc

可以输入conda来检查，因为其后没有加具体的东西，会出现大段提示，报错，则没有激活
（5）添加镜像
直接复制粘贴到命令行，回车

# 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

(来源：生信星球)

(base) bio18@VM-0-10-ubuntu:~/biosoft$ 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(base)

Ready!

2. conda基本操作

查看当前所有列表 conda list

(base) bio18@VM-0-10-ubuntu:~/biosoft$ conda list
# packages in environment at /home/bio18/miniconda3:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main    defaults
asn1crypto                1.3.0                    py37_0    defaults
ca-certificates           2020.1.1                      0    defaults

后面还很多

搜索软件 conda search fastqc

(base) bio18@VM-0-10-ubuntu:~/biosoft$ conda search fastqc
Loading channels: done
# Name                       Version           Build  Channel
fastqc                        0.10.1               0  anaconda/cloud/bioconda
fastqc                        0.10.1               1  anaconda/cloud/bioconda
fastqc                        0.11.2               1  anaconda/cloud/bioconda
fastqc                        0.11.2      pl5.22.0_0  anaconda/cloud/bioconda
fastqc                        0.11.3               0  anaconda/cloud/bioconda
fastqc                        0.11.3               1  anaconda/cloud/bioconda
fastqc                        0.11.4               0  anaconda/cloud/bioconda
fastqc                        0.11.4               1  anaconda/cloud/bioconda
fastqc                        0.11.4               2  anaconda/cloud/bioconda
fastqc                        0.11.5               1  anaconda/cloud/bioconda
fastqc                        0.11.5               4  anaconda/cloud/bioconda
fastqc                        0.11.5      pl5.22.0_2  anaconda/cloud/bioconda

以fastqc为例

安装软件 conda install fastqc -y -y自动安装，没有则会出现问你可不可以

Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.2
  latest version: 4.8.3

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /home/bio18/miniconda3

自动安装最新

卸载软件 conda remove fasty -y

(base) bio18@VM-0-10-ubuntu:~/biosoft$ conda remove fastqc -y
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/bio18/miniconda3

  removed specs:
    - fastqc


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    _libgcc_mutex-0.1          |      conda_forge           3 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge

3. conda选修操作

来源：生信星球

（懒懒怕迷路）

查看conda当前环境 conda info --envs

(base) bio18@VM-0-10-ubuntu:~/biosoft$ conda info --envs
# conda environments:
#
base                  *  /home/bio18/miniconda3

前面带*为默认

建立一个处理转录组的环境rna-seq,指定python版本是3，安装软件fastqc、trimmmomatic
conda create -n rna-seq python=3 fastqc trimmomatic -y

Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/bio18/miniconda3/envs/rna-seq

  added / updated specs:
    - fastqc
    - python=3
    - trimmomatic


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    certifi-2020.4.5.1         |   py38h32f6830_0         151 KB  https://mirrors

检查环境

(base) bio18@VM-0-10-ubuntu:~/biosoft$ conda info --envs
# conda environments:
#
base                  *  /home/bio18/miniconda3
rna-seq                  /home/bio18/miniconda3/envs/rna-seq

激活新环境 conda activate rna-seq

(base) bio18@VM-0-10-ubuntu:~/biosoft$ conda activate rna-seq
(rna-seq) bio18@VM-0-10-ubuntu:~/biosoft$ fastqc
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)

(rna-seq)在用户名前，输入fastqc,有提示——成功

学习小组Day3笔记——懒懒

linux如何安装软件.png

1. 了解conda

2. 安装miniconda

2. conda基本操作

3. conda选修操作

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