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 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