CGAT - Computational Genomics Analysis Tools安装

环境：CentOS 6.5

因为CentOS默认需要python2.7，所以先安装python2.7。

方法参考：

./configure --prefix=/usr/local   

make && make altinstall

因为yum依赖于python2.6，所以需要altinstall。

https://www.digitalocean.com/community/articles/how-to-set-up-python-2-7-6-and-3-3-3-on-centos-6-4

安装必须包：

yum groupinstall -y 'development tools'

yum install -y zlib-dev openssl-devel sqlite-devel bzip2-devel

yum install gcc-gfortran blas-devel lapack-devel

安装setuptools。

# Let's download the installation file using wget:
wget --no-check-certificate https://pypi.python.org/packages/source/s/setuptools/setuptools-1.4.2.tar.gz

# Extract the files from the archive:
tar -xvf setuptools-1.4.2.tar.gz

# Enter the extracted directory:
cd setuptools-1.4.2

# Install setuptools using the Python we've installed (2.7.6)
python2.7 setup.py install

下载pip。

curl https://raw.github.com/pypa/pip/master/contrib/get-pip.py | python2.7 -

安装bx-python。

easy_install https://bitbucket.org/james_taylor/bx-python/get/tip.tar.bz2

官方网站上下载cgat。

https://github.com/CGATOxford/cgat

源码编译bedtools

产生的程序统一放置/usr/local/bin

boost库源代码方式安装(不安装会影响到alignlib的安装)

参考 http://nyc1991.blog.51cto.com/6424159/1133388

./configure

./b2 --prefix=/usr/local install

R编译安装

Rpy2安装

http://compbio.tongji.edu.cn/~sunhf/?p=124

pip方式安装依赖包

pip2.7 install cython

pip2.7 install numpy

pip2.7 install pysam

pip2.7 install https://bitbucket.org/james_taylor/bx-python/get/tip.tar.bz2

pip2.7 install biopython

pip2.7 install pybedtools

pip install matplotlib

pip install scrpy

最后通过pip安装cgat

pip2.7 install cgat

程序最后被安装到/usr/local/cgat