conda 虚拟环境内安装git_用anaconda创建的虚拟环境安装FALCON

参考资料

1、用anaconda创建Python2的虚拟环境

$ conda create -n py2 python=2*

2、激活虚拟环境

$source activate py2

3、查看虚拟Python2的位置

$which python

~/software/anaconda3/envs/py2/bin/python

4、按照github上安装FALCON的流程安装FALCON

$git clone git://github.com/PacificBiosciences/FALCON-integrate.git

$cd FALCON-integrate

$git submodule update –init

$cd pypeFLOW

$python setup.py install

$cd ..

$cd FALCON

$python setup.py install

$cd ..

$cd DAZZ_DB/

$make

$cp DBrm DBshow DBsplit DBstats DBdump fasta2DB ~/software/anaconda3/envs/py2/bin/

$cd ..

$cd DALIGNER

$make

$cp daligner daligner_p DB2Falcon HPCdaligner LA4Falcon LAmerge LAsort ~/software/anaconda3/envs/py2/bin/

$cd ..

5、然后可执行的fc_run.py文件就在~/software/anaconda3/envs/py2/bin/里面.

$cd ~/software/anaconda3/envs/py2/bin

$python fc_run.py –h

usage: fc_run.py [-h] config [logger]

positional arguments:

config      .cfg/.ini/.json

logger      (Optional)JSON config for standard Python logging module

optional arguments:

-h, --help  show this help message and exit