参考官方github： https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries

(1) 选择用virtualenv and install External dependencies

export PYTHONUSERBASE=/home/yanbo/py36-yanbo

tar xvzf /home/yanbo/software/falcon-2018.08.08-21.41-py2.7-ucs4-beta.tar.gz -C /home/yanbo/py36-yanbo/

export LD_LIBRARY_PATH=/home/yanbo/py36-yanbo/lib:${LD_LIBRARY_PATH}

export PATH=/home/yanbo/py36-yanbo/bin:${PATH}

#export PYTHONPATH=/home/yanbo/py36-yanbo/lib/python2.7/site-packages

#unset PYTHONPATH

External dependencies:

samtools: http://www.htslib.org/download/

minimap2:https://github.com/lh3/minimap2/blob/master/cookbook.md#intro

which samtools 

samtools --help 

pbalign --help 

variantCaller -h 

python2.7 -c 'import pysam; print pysam' 

python2.7 -c 'import falcon_unzip; print falcon_unzip'

Fail: above tests not pass

(2) userbase

Pass tests in (1) ; 

when run it I found it is a python3 enviroment not python2 and faclon only support python2.

(2.1) intall python2.7.10 in py2-yanbo

https://www.cnblogs.com/smileyes/p/7288487.html

wget https://www.python.org/ftp/python/2.7.10/Python-2.7.10.tgz

tar xvf Python-2.7.10.tgz

cd Python-2.7.10

./configure --prefix=/home/yanbo/py2-yanbo

make make install

make distclean

Python-2.7.10 版本太旧

pbalign --help not pass cause import hashlib meet problem

export PYTHONUSERBASE=/home/yanbo/py2-yanbo

tar xvzf /home/yanbo/software/falcon-2018.08.08-21.41-py2.7-ucs4-beta.tar.gz -C /home/yanbo/py2-yanbo/

export LD_LIBRARY_PATH=/home/yanbo/py2-yanbo/lib:${LD_LIBRARY_PATH}

export PATH=/home/yanbo/py2-yanbo/bin:${PATH}

#export PYTHONPATH=/home/yanbo/py2-yanbo/lib/python2.7/site-packages

(2.1.1) intall python2.7.15 in py36-yanbo

https://www.cnblogs.com/jessepeng/p/11610051.html

import hashlib problem solve

but variantCaller -h can find python-consensuscore also numpy and pysam need pip install

pip install numpy

pip install pysam

(3) install miniconda2 (install python2.7.15 )

export PYTHONUSERBASE=/home/yanbo/py36-yanbo/miniconda2

tar xvzf /home/yanbo/software/falcon-2018.08.08-21.41-py2.7-ucs4-beta.tar.gz -C /home/yanbo/py36-yanbo/miniconda2

export LD_LIBRARY_PATH=/home/yanbo/py36-yanbo/miniconda2/lib:${LD_LIBRARY_PATH}

export PATH=/home/yanbo/py36-yanbo/miniconda2/bin:${PATH}

#export PYTHONPATH=/home/yanbo/py36-yanbo/miniconda2/lib/python2.7/site-packages

conda install -c bioconda python-consensuscore

至此成功安装falcon and falcon-unzip

------------------------------------------- conda 的使用

conda install -c bioconda flye

conda update flye

/home/yanbo/py36-yanbo/miniconda2/bin/flye  --version 2.3.1-release