1. 寻找软件所在的镜像

用conda安装软件的标准语法格式为：

$ conda install -c <channel> <software>

其中-c这个参数很重要，通过它来指定软件下载的镜像位置

对于我们这些生物信息学的从业人员来说，最常用的channel（这里可以理解成镜像）就是bioconda了，如果想要安装生物信息学，一般都会先到 bioconda官网上找一找自己想要的软件在不在bioconda的官方镜像的列表中

这里以搜索BWA为例

如果软件正好在bioconda官方镜像里，万事大吉，直接用下面的命令安装就可以了

$ conda install -c bioconda bwa

如果你已经将bioconda这个channel加到自己的默认channel列表中，则不指定-c参数也可以

但是如果你要的软件不在bioconda中怎么办？

这时你可以通过执行 anaconda search -t <software>来列出保存目标软件的所有官方镜像

比如，如果你要安装CNVnator（这是一个安装过程神级坑的软件），它就不在bioconda中，执行

$ anaconda search -t cnvnator

得到的检索结果如下：

Using binstar api site https://api.anaconda.org
Run 'anaconda show <USER/PACKAGE>' to get more details:
Packages:
     Name                      |  Version | Package Types   | Platforms
     ------------------------- |   ------ | --------------- | ---------------
     pwwang/cnvnator           |    0.3.3 | conda           | linux-64
                                          : a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
Found 1 packages

通过上面的检索结果我们就知道目前只有唯一一个保存CNVnator的conda镜像，为pwwang，这是就可以通过指定刚才找到的镜像完成软件的安装了：

$ conda install -c pwwang cnvnator

2. conda中的Python与系统自带的Python打架

在你安装完conda（不论是Anaconda还是Miniconda），它会自带安装对应的Python版本，而你的系统原先也安装了Python，这时两个来源两个版本的Python会发生冲突，使得你新安装的conda运行报错，比如简单地运行 conda list，会出现以下一长串的报错信息：

Error processing line 1 of /usr/local/lib/python2.7/site-packages/matplotlib-2.1.2-py2.7-nspkg.pth:

Fatal Python error: initsite: Failed to import the site module
Traceback (most recent call last):
  File "/disk2/yut/SOFTWARE/miniconda3/lib/python3.7/site.py", line 168, in addpackage
    exec(line)
  File "<string>", line 1, in <module>
  File "/disk2/yut/SOFTWARE/miniconda3/lib/python3.7/importlib/util.py", line 14, in <module>
    from contextlib import contextmanager
  File "/disk2/yut/SOFTWARE/miniconda3/lib/python3.7/contextlib.py", line 5, in <module>
    from collections import deque
  File "/disk2/yut/SOFTWARE/miniconda3/lib/python3.7/collections/__init__.py", line 27, in <module>
    from reprlib import recursive_repr as _recursive_repr
  File "/usr/local/lib/python2.7/site-packages/reprlib/__init__.py", line 7, in <module>
    raise ImportError('This package should not be accessible on Python 3. '
ImportError: This package should not be accessible on Python 3. Either you are trying to run from the python-future src folder or your installation of python-future is corrupted.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python2.7/site-packages/site.py", line 73, in <module>
    __boot()
  File "/usr/local/lib/python2.7/site-packages/site.py", line 47, in __boot
    addsitedir(item)
  File "/disk2/yut/SOFTWARE/miniconda3/lib/python3.7/site.py", line 207, in addsitedir
    addpackage(sitedir, name, known_paths)
  File "/disk2/yut/SOFTWARE/miniconda3/lib/python3.7/site.py", line 178, in addpackage
    import traceback
  File "/disk2/yut/SOFTWARE/miniconda3/lib/python3.7/traceback.py", line 3, in <module>
    import collections
  File "/disk2/yut/SOFTWARE/miniconda3/lib/python3.7/collections/__init__.py", line 27, in <module>
    from reprlib import recursive_repr as _recursive_repr
  File "/usr/local/lib/python2.7/site-packages/reprlib/__init__.py", line 7, in <module>
    raise ImportError('This package should not be accessible on Python 3. '
ImportError: This package should not be accessible on Python 3. Either you are trying to run from the python-future src folder or your installation of python-future is corrupted.

仔细阅读上面的报错信息，你会发现这就是系统的Python和conda里的Python冲突了（我喜欢称这种现象为掐架、打架），这也是conda这个软件安装神器在给你带来方便的同时带来的副产品：它会污染你的环境变量！

遇到两个Python环境冲突的情况，我一般的解决情况就是，关闭系统的Python，即将系统的Python路径从我的环境变量中删除