刚出生的 Ubuntu 趁热安装 Anaconda3，配置metapi

刚出生的 Ubuntu 趁热安装 Anaconda3，配置metapi

2022-05-25
之前的服务器到期了，呜呜呜。
所以把腾讯云上海的轻量服务器从 win 重装成了 Ubuntu 18，一张白纸，啥也没有，为了跑宏基因组分析，先装一个Anaconda3。

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下载&安装 Anaconda3

下载 Anaconda3

先建一个路径，然后下载 Anaconda3，以轻量服务器的带宽大概几分钟。

wget https://mirrors.tuna.tsinghua.edu.cn/anaconda/archive/Anaconda3-2021.11-Linux-x86_64.sh

查看文件：

ubuntu@VM-16-13-ubuntu:~/Down_sw/25-05-2022$ ls
Anaconda3-2021.11-Linux-x86_64.sh

安装 Anaconda3

bash Anaconda3-2021.11-Linux-x86_64.sh

一路回车，然后yes，回车

Please answer 'yes' or 'no':'
>>> yes

Anaconda3 will now be installed into this location:
/home/ubuntu/anaconda3

  - Press ENTER to confirm the location
  - Press CTRL-C to abort the installation
  - Or specify a different location below

[/home/ubuntu/anaconda3] >>>
PREFIX=/home/ubuntu/anaconda3
Unpacking payload ...
Extracting : sniffio-1.2.0-py39h06a4308_1.conda:  40%|████████████▎                  | 154/389 [00:09<00:17, 13.26it/s]

继续yes

installation finished.
Do you wish the installer to initialize Anaconda3
by running conda init? [yes|no]
[no] >>> yes
no change     /home/ubuntu/anaconda3/condabin/conda
no change     /home/ubuntu/anaconda3/bin/conda
no change     /home/ubuntu/anaconda3/bin/conda-env
no change     /home/ubuntu/anaconda3/bin/activate
no change     /home/ubuntu/anaconda3/bin/deactivate
no change     /home/ubuntu/anaconda3/etc/profile.d/conda.sh
no change     /home/ubuntu/anaconda3/etc/fish/conf.d/conda.fish
no change     /home/ubuntu/anaconda3/shell/condabin/Conda.psm1
no change     /home/ubuntu/anaconda3/shell/condabin/conda-hook.ps1
no change     /home/ubuntu/anaconda3/lib/python3.9/site-packages/xontrib/conda.xsh
no change     /home/ubuntu/anaconda3/etc/profile.d/conda.csh
modified      /home/ubuntu/.bashrc

==> 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 Anaconda3!

===========================================================================

Working with Python and Jupyter notebooks is a breeze with PyCharm Pro,
designed to be used with Anaconda. Download now and have the best data
tools at your fingertips.

PyCharm Pro for Anaconda is available at: https://www.anaconda.com/pycharm

ubuntu@VM-16-13-ubuntu:~/Down_sw/25-05-2022$

source 一下，出现 (base) 环境

ubuntu@VM-16-13-ubuntu:~/Down_sw/25-05-2022$ conda
conda: command not found
ubuntu@VM-16-13-ubuntu:~/Down_sw/25-05-2022$ source ~/.bashrc
(base) ubuntu@VM-16-13-ubuntu:~/Down_sw/25-05-2022$

conda deactivate 退出 (base) 环境

想要升级 conda：

conda update -n base -c defaults conda

结果：

The following packages will be UPDATED:

  conda                               4.10.3-py39h06a4308_0 --> 4.12.0-py39h06a4308_0
  conda-package-han~                   1.7.3-py39h27cfd23_1 --> 1.8.1-py39h7f8727e_0

创建虚拟环境

metapi已经2.1.1版本了，https://anaconda.org/bioconda/metapi

创建名为 skin 的虚拟环境，python 版本为 3.7(先试一试)

conda create -n skin python=3.7

ubuntu@VM-16-13-ubuntu:~/Down_sw/25-05-2022$ conda activate skin
(skin) ubuntu@VM-16-13-ubuntu:~/Down_sw/25-05-2022$

vim ~/.bashrc 加快捷命令

alias skin='conda activate skin'

常用conda 命令

#创建虚拟环境
conda create -n your_env_name python=X.X（3.6、3.7等）
#激活虚拟环境
source activate your_env_name(虚拟环境名称)
#退出虚拟环境
source deactivate your_env_name(虚拟环境名称)
#删除虚拟环境
conda remove -n your_env_name(虚拟环境名称) --all
#查看安装了哪些包
conda list
 
#安装包
conda install package_name(包名)
conda install scrapy==x.x # 安装指定版本的包
conda install -n 环境名 包名 # 在conda指定的某个环境中安装包
 
#查看当前存在哪些虚拟环境
conda env list 
#或 
conda info -e

参考：https://blog.csdn.net/qq_52813185/article/details/124826603

pip更新：

python -m pip install --upgrade pip

安装metapi

刚更新的 2.1.1 ，真热乎啊，要是早一天就好了，昨天本地配置最后发现有依赖项不支持win64很难受，今天先在Ubuntu上试一试。

pip3 install metapi==2.1.1

测试，报错：

(skin) ubuntu@VM-16-13-ubuntu:~/Down_sw/25-05-2022$ metapi --help
Traceback (most recent call last):
  File "/home/ubuntu/anaconda3/envs/skin/bin/metapi", line 5, in <module>
    from metapi.corer import main
  File "/home/ubuntu/anaconda3/envs/skin/lib/python3.7/site-packages/metapi/__init__.py", line 25, in <module>
    from metapi.qcer import change
  File "/home/ubuntu/anaconda3/envs/skin/lib/python3.7/site-packages/metapi/qcer.py", line 5, in <module>
    import seaborn as sns
ModuleNotFoundError: No module named 'seaborn'

安装所缺依赖：

pip install seaborn

成功：

(skin) ubuntu@VM-16-13-ubuntu:~/Down_sw/25-05-2022$ metapi --help
usage: metapi [-h] [-v]  ...

 .___  ___.  _______ .___________.    ___      .______    __
 |   \/   | |   ____||           |   /   \     |   _  \  |  |
 |  \  /  | |  |__   `---|  |----`  /  ^  \    |  |_)  | |  |
 |  |\/|  | |   __|      |  |      /  /_\  \   |   ___/  |  |
 |  |  |  | |  |____     |  |     /  _____  \  |  |      |  |
 |__|  |__| |_______|    |__|    /__/     \__\ | _|      |__|

           Omics for All, Open Source for All

A general metagenomics data mining system focus on robust microbiome research

optional arguments:
  -h, --help     show this help message and exit
  -v, --version  print software version and exit

available subcommands:

跟作者反馈一下：

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