Conda的安装

下载+安装Conda

• 清华镜像下载

#首先创建一个文件夹src（源代码的意思），将下载的软件保存到其中
#下载Miniconda3.4
 wget -c https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh

#下载完成后，安装：
vip39@VM-0-15-ubuntu:~/src$ bash Miniconda3-4.5.11-Linux-x86_64.sh 

# 一直默认，直到...
installation finished.
Do you wish the installer to prepend the Miniconda3 install location
to PATH in your /home/vip39/.bashrc ? [yes|no]
[no] >>> 
# 选择no：推荐是这样，防止后期变量冲突

# 启动：
vip39@VM-0-15-ubuntu:~/src$ source ~/miniconda3/bin/activate
(base) vip39@VM-0-15-ubuntu:~/src$ 
# 会发现前面多了个（base），表示目前处于conda环境
#

查找bwa：

(base) vip39@VM-0-15-ubuntu:~/src$ conda search bwa
Loading channels: done

PackagesNotFoundError: The following packages are not available from current channels:

  - bwa

Current channels:

  - https://repo.anaconda.com/pkgs/main/linux-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/linux-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/linux-64
  - https://repo.anaconda.com/pkgs/r/noarch
  - https://repo.anaconda.com/pkgs/pro/linux-64
  - https://repo.anaconda.com/pkgs/pro/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page

下载anaconda

• 到清华镜像下载：

1. Anaconda的仓库镜象
2. Conda的三方源：Conda Forage ；bioconda

#查看环境变量：
(base) vip39@VM-0-15-ubuntu:~/src$ vim ~/.condarc
# 目前有的channels：
channels:
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
  - defaults
show_channel_urls: true
# bioconda需要放在第一位，优先搜索软件；forge第二位

学习conda的基本操作：

# 搜索bwa软件
(base) vip39@VM-0-15-ubuntu:~/src$ conda search bwa
# 上面这个步骤将耗费时间：

# 下载bwa：-y表示其余默认
(base) vip39@VM-0-15-ubuntu:~/src$ conda install bwa -y
Solving environment:... #帮我们解决环境变量的问题

• 下载samtools：

(base) vip39@VM-0-15-ubuntu:~/src$ conda install samtools=1.8 -y
# 1.8 表示samtools的版本号

#运行samtools，可以直接输入samtools，因为：
(base) vip39@VM-0-15-ubuntu:~/src$ source ~/miniconda3/bin/activate 
# 这一步实现了如下：
(base) vip39@VM-0-15-ubuntu:~/src$ echo $PATH
/home/vip39/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
# minconda3存在于我们的环境变量中了

创建软链接：

# 退出目前环境：
(base) vip39@VM-0-15-ubuntu:~/src$ source deactivate
vip39@VM-0-15-ubuntu:~/src$ echo $PATH
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
# 这个时候直接的samtools是不能安装的（其实我是可以的），那么可以：
# 通过软件实际路径进行：
vip39@VM-0-15-ubuntu:~/src$ ~/miniconda3/bin/samtools

# 或者可以创建软链接：
# samtools问题待解决

conda 的环境变量

(base) vip39@VM-0-15-ubuntu:~$ conda info --envs
# conda environments:
#
base                  *  /home/vip39/miniconda3

# 目前为miniconda3，支持的是python2；
# 想要安装macs2（python2环境下进行的）；需要建立一个python2的环境
# 不要直接安装，否则会把python3变成python2，导致后期的报错。
# 建立python2的环境：
(base) vip39@VM-0-15-ubuntu:~$ conda create -n python2 python=2
...
#
# To activate this environment, use
#
#     $ conda activate python2 #表示启动python2的环境
#
# To deactivate an active environment, use
#
#     $ conda deactivate

(base) vip39@VM-0-15-ubuntu:~$ conda activate python2
(python2) vip39@VM-0-15-ubuntu:~$

# 目前python2的环境下安装macs2：
(python2) vip39@VM-0-15-ubuntu:~$ conda install macs2
# 查看一下macs2的环境变量：
(python2) vip39@VM-0-15-ubuntu:~$ which macs2
/home/vip39/miniconda3/envs/python2/bin/macs2

# 启动macs2的方法：
(python2) vip39@VM-0-15-ubuntu:~$ source deactivate
(base) vip39@VM-0-15-ubuntu:~$ masc2
No command 'masc2' found, did you mean:
 Command 'macs2' from package 'macs' (universe)
masc2: command not found
(base) vip39@VM-0-15-ubuntu:~$ ~/miniconda3/envs/python2/bin/macs2 
usage: macs2 [-h] [--version]
             {callpeak,bdgpeakcall,bdgbroadcall,bdgcmp,bdgopt,cmbreps,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak}
             ...
macs2: error: too few arguments
(base) vip39@VM-0-15-ubuntu:~$ ln -s ~/miniconda3/envs/python2/bin/macs2 ~/.local/bin/
(base) vip39@VM-0-15-ubuntu:~$ macs2
The program 'macs2' is currently not installed. To run 'macs2' please ask your administrator to install the package 'macs'