“生信星球（wx:babyfox2017）”的课程学习笔记。
conda相当于App Store，通过conda进行其他软件的安装。做生信安装miniconda即可。
1.下载/安装/激活miniconda
1. 在终端unman -a，确定系统类型及位数。
系统版本确定
2. 下载miniconda
用搜索引擎搜索“miniconda 清华”，打开清华镜像网站。
搜索conda 清华
进入页面，找到miniconda下载界面。
miniconda下载链接
进入下载界面，找到符合系统要求的miniconda版本的最新版，右击-复制链接。
注意，conda是装在服务器中的，所以要看服务器的系统版本，和本地电脑系统无关。
屏幕快照 2020-05-10 上午11.56.02.png
进入欲存储路径，这里是/home/bio01/biosoft，在终端用
wget命令，复制链接内容，回车，即开始下载miniconda。
wget https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-py38_4.8.2-Linux-x86_64.sh
完成下载miniconda
- .sh是脚本，可运行软件，我理解为安装包。即便后面安装出现问题，只要安装包在，就可以重新开始安装。
3. 安装miniconda
命令bash Miniconda3-py38_4.8.2-Linux-x86_64.sh，即bash+脚本名称，回车后，安装开始，让写yes就yes，让Enter就Enter。License Agreement里有好多东西，不用看，一直按Enter向下就可以了。
bio01@VM-0-10-ubuntu:~/biosoft$ bash Miniconda3-py38_4.8.2-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
>>>
===================================
End User License Agreement - Anaconda Individual Edition
===================================
Copyright 2015-2020, Anaconda, Inc.
All rights reserved under the 3-clause BSD License:
This End User License Agreement (the "Agreement") is a legal agreement between you and Anaconda
, Inc. ("Anaconda") and governs your use of Anaconda Individual Edition (which was formerly kno
wn as Anaconda Distribution).
Subject to the terms of this Agreement, Anaconda hereby grants you a non-exclusive, non-transfe
rable license to:
* Install and use the Anaconda Individual Edition (which was formerly known as Anaconda Distr
ibution),
* Modify and create derivative works of sample source code delivered in Anaconda Individual E
dition; and
* Redistribute code files in source (if provided to you by Anaconda as source) and binary for
ms, with or without modification subject to the requirements set forth below.
直到出现问yes/no时，输入yes。后面依然是Enter。
安装过程
最后出现Thank you ……即安装成功。
==> For changes to take effect, close and re-open your current shell. <==
If you'd prefer that conda's base environment not be activated on startup,
set the auto_activate_base parameter to false:
conda config --set auto_activate_base false
Thank you for installing Miniconda3!
4. 激活
输入命令source ～/.bashrc，回车。
再输入conda，回车，出现一大堆信息，即为激活成功。
bio01@VM-0-10-ubuntu:~/biosoft$ source ~/.bashrc
(base) bio01@VM-0-10-ubuntu:~/biosoft$ conda
usage: conda [-h] [-V] command ...
conda is a tool for managing and deploying applications, environments and packages.
Options:
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.
conda commands available from other packages:
env
5. 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
到此为止，conda安装并激活成功，可以开始使用。
2. Conda的使用
1. 查看当前软件列表
conda list
2. 搜索软件
conda search 软件名
(base) bio01@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
fastqc 0.11.5 pl5.22.0_3 anaconda/cloud/bioconda
fastqc 0.11.6 2 anaconda/cloud/bioconda
fastqc 0.11.6 pl5.22.0_0 anaconda/cloud/bioconda
fastqc 0.11.6 pl5.22.0_1 anaconda/cloud/bioconda
fastqc 0.11.7 4 anaconda/cloud/bioconda
fastqc 0.11.7 5 anaconda/cloud/bioconda
fastqc 0.11.7 6 anaconda/cloud/bioconda
fastqc 0.11.7 pl5.22.0_0 anaconda/cloud/bioconda
fastqc 0.11.7 pl5.22.0_2 anaconda/cloud/bioconda
fastqc 0.11.8 0 anaconda/cloud/bioconda
fastqc 0.11.8 1 anaconda/cloud/bioconda
fastqc 0.11.8 2 anaconda/cloud/bioconda
fastqc 0.11.9 0 anaconda/cloud/bioconda
3. 安装软件
conda install 软件名 -y -y表示自动安装，不加-y就需要来回答一些yes/no的问题。
conda install 软件名=版本号 -y可指定安装版本。
conda install fastqc=0.11.17
4. 卸载软件
conda remove 软件名 -y
3. conda环境
我们处理不同数据时，可以创建不同的环境，使安装的软件、数据互相不影响。
1. 查看当前环境
conda info --envs，可以看到现在只有一个默认环境。
(base) bio01@VM-0-10-ubuntu:~/miniconda3$ conda info --envs
# conda environments:
#
base * /home/bio01/miniconda3
2. 新建一个环境
create -n 环境名 python= 版本 软件名 软件名 …… -y，创建环境，确定python版本，并安装几种软件。
新建环境
此时，用conda info --envs查看信息，可以看到新增了一个rna-seq环境。
(base) bio01@VM-0-10-ubuntu:~/miniconda3$ conda info --envs
# conda environments:
#
base * /home/bio01/miniconda3
rna-seq /home/bio01/miniconda3/envs/rna-seq
3. 激活新环境
activate conda 环境名，root前出现新环境名。
再输入fastqc，可以看到出现一些信息，说明新环境被激活，并且软件可以使用。
(base) bio01@VM-0-10-ubuntu:~/miniconda3$ conda activate rna-seq
(rna-seq) bio01@VM-0-10-ubuntu:~/miniconda3$ 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)
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)
