一、基本使用

1. 创建和安装

创建flye环境

安装numpy包到flye环境

conda install -n flye numpy

创建一个名为flye的环境，并安装Python版本3.6（conda自动寻找3.6.x中最新版本）

conda create -n flye python=3.6

2. 使用

安装好后，使用activate激活某个环境

source activate flye
conda activate flye (更新conda可使用)

退出已激活的环境

source deactivate flye
conda deactivate flye (更新conda可使用)

3. 删除

删除flye环境和其环境所有的包

conda remove -n flye --all

移除flye环境的 Sambamba

conda remove -n flye sambamba

4. 查看

查看当前存在的环境

conda info --envs

查看已经安装的packages

【最新版的conda是从site-packages文件夹中搜索已经安装的包，不依赖pip，因此可以显示出通过各种方式安装的包】
conda list

查看flye环境中已安装包

conda list -n flye

5. 更新

更新conda，保持conda最新

conda update conda

更新flye中的numpy包

conda update -n flye numpy

6. 配置

添加环境

conda config --add envs_dirs /opt/anaconda/envs/flye_test

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

二、高级用法

1. 复制环境到新电脑或者用户（clone）

输出环境信息到文本

conda env export -n hicExplorer > environment.yml

依照文本信息重新生成一个同样环境

conda env create -f environment.yml

比如

依照文本信息重新生成 training环境
conda env create -n training -f environment.yml

2. root安装一次，多用户共享

参考(验证是正确的)：http://www.dxulab.org/wiki/anacondaenvformulti-users

sudo su -
adduser anaconda
bash Anaconda3-2019.03-Linux-x86_64.sh -b -p /opt/anaconda
chown -R anaconda:anaconda /opt/anaconda
chmod -R go-w /opt/anaconda
chmod -R go+rX /opt/anaconda

# And then you can put  /opt/anaconda/bin in the PATH added in /etc/profiles.d/anaconda.sh (or wherever). A (very) nice thing about Anaconda is that it requires no environment variables to be set. Adding it to your PATH is just for convenience.

# You (as the sudo-empowered admin) can then go and create new environments for all users on the system:

sudo -u anaconda /opt/anaconda/bin/conda env create -n flye_test -c bioconda flye
sudo -u anaconda /opt/anaconda/bin/conda env create -n training -f environment.base.yml

# And then any user, say janesmith can go and use these:

source activate coolscience # will add /opt/anaconda/envs/coolscience/bin to PATH
# Additionally they can create their own envs:

conda create -n webdev django flask sqlalchemy pylons
# which will (should) be created in ~janesmith/.conda/envs/webdev.

# I have tested exactly 0% of the commands above, but they should point you in the right direction. Additionally, I must note, Conda is known to have “gotchas” that can come up when using it in a multi-user environment like this. A partial record of the challenges you may face are recorded in this issue:

3. root安装一次，多用户共（无患子服务器），发现无需新增用户anaconda以及将文件归属anaconda，普通用户也能成功调用

sudoer 用户切换后，运行如下命令:

sudo -s
bash Anaconda3-2019.03-Linux-x86_64.sh -b -p /opt/anaconda

其中environment.flye.yml和environment.base.yml是在虚拟机中环境的导出文件

conda env export -n flye > environment.flye.yml
conda env export -n base > environment.base.yml

依照创建创建环境flye_test和training，

/opt/anaconda/bin/conda env create -n flye_test -f environment.flye.yml
/opt/anaconda/bin/conda env create -n training -f environment.base.yml

普通用户调用环境

方法1：

进入某个环境source /opt/anaconda/bin/activate flye_test

[junting_feng@localhost ~]$ /opt/anaconda/bin/conda info --envs
# conda environments:
#
base                  *  /opt/anaconda
flye_test                /opt/anaconda/envs/flye_test

[junting_feng@localhost ~]$ source /opt/anaconda/bin/activate flye_test
(flye_test) [junting_feng@localhost ~]$

退出当前环境source /opt/anaconda/bin/deactivate，忽略报错

(flye_test) [smrtanalysis@localhost ~]$ source /opt/anaconda/bin/deactivate
DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'.
[smrtanalysis@localhost ~]$

方法2：

执行/opt/anaconda/bin/conda activate flye_test遇到如下报错：

[zaohai_zeng@localhost ~]$ /opt/anaconda/bin/conda activate flye_test

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run

    $ conda init <SHELL_NAME>

Currently supported shells are:
  - bash
  - fish
  - tcsh
  - xonsh
  - zsh
  - powershell

See 'conda init --help' for more information and options.

IMPORTANT: You may need to close and restart your shell after running 'conda init'.

按照提示运行 /opt/anaconda/bin/conda init命令，将conda写入.bashrc文件

(base) [zaohai_zeng@localhost ~]$ /opt/anaconda/bin/conda init
no change     /opt/anaconda/condabin/conda
no change     /opt/anaconda/bin/conda
no change     /opt/anaconda/bin/conda-env
no change     /opt/anaconda/bin/activate
no change     /opt/anaconda/bin/deactivate
no change     /opt/anaconda/etc/profile.d/conda.sh
no change     /opt/anaconda/etc/fish/conf.d/conda.fish
no change     /opt/anaconda/shell/condabin/Conda.psm1
no change     /opt/anaconda/shell/condabin/conda-hook.ps1
no change     /opt/anaconda/lib/python3.7/site-packages/xontrib/conda.xsh
no change     /opt/anaconda/etc/profile.d/conda.csh
modified      /home/zaohai_zeng/.bashrc

==> For changes to take effect, close and re-open your current shell. <==

4. 退出，并重新登录

进入环境 conda activate flye_test

(base) [zaohai_zeng@localhost ~]$ conda activate flye_test
(flye_test) [zaohai_zeng@localhost ~]$

退出环境 conda deactivate

(flye_test) [zaohai_zeng@localhost ~]$ conda deactivate
(base) [zaohai_zeng@localhost ~]$