Scientific Linux 6.X Installation¶
Scientific Linux is a Red Hat Enterprise Linux-based operating system and therefore the instructions below should apply to all other derivatives as well.
The Quick installation uses CGAT supplied scripts for installation, while Manual installation lists all the steps individually.
Quick installation¶
Get a copy of the installation scripts¶
Download and place them into your home directory:
cd
wget https://raw.github.com/CGATOxford/cgat/master/requires.txt
wget https://raw.github.com/CGATOxford/cgat/master/setup-RPMs.sh
wget https://raw.github.com/CGATOxford/cgat/master/setup-CGAT.sh
Install RPM dependencies¶
Become root (or ask your system administrator to do it for you) and run setup-RPMs.sh:
./setup-RPMs.sh
Install a Python virtual environment with the CGAT code collection¶
Do not be root for this step and run setup-CGAT.sh:
./setup-CGAT.sh
Test the installation¶
First activate the CGAT virtual environment:
source $HOME/CGAT/virtualenv-1.10.1/cgat-venv/bin/activate
Then, test the cgat command:
cgat --help
Finish the CGAT virtual environment¶
When you are done, you may deactivate the CGAT virtual environment:
deactivate
Manual installation¶
Install RPM dependencies¶
You can either install them one by one or all at the same time with yum:
yum install gcc # required by python
yum install zlib-devel # required by virtualenv
yum install openssl-devel # required by pip
yum install bzip2-devel # required by bx-python
yum install gcc-c++ # required by pybedtools
yum install freetype-devel # required by matplotlib
yum install libpng-devel # required by matplotlib
yum install blas atlas lapack # required by scipy
yum install gcc-gfortran # required by scipyi
yum install postgresql-devel # required by PyGreSQL
yum install R-core-devel # required by rpy2
yum install readline-devel # required by rpy2
yum install mysql-devel # required by MySQL-python
yum install boost-devel # required by alignlib
yum install sqlite-devel # required by CGAT
Please note that you may also need the EPEL (Extra Packages for Enterprise Linux) repository to install R:
yum install epel-release
Now type this additional commands to get scipy working:
ln -s /usr/lib64/libblas.so.3 /usr/lib64/libblas.so
ln -s /usr/lib64/libatlas.so.3 /usr/lib64/libatlas.so
ln -s /usr/lib64/liblapack.so.3 /usr/lib64/liblapack.so
Build Python 2.7.5¶
Download and build your own, isolated Python installation:
cd
mkdir CGAT
wget http://www.python.org/ftp/python/2.7.5/Python-2.7.5.tgz
tar xzvf Python-2.7.5.tgz
rm Python-2.7.5.tgz
cd Python-2.7.5
./configure --prefix=$HOME/CGAT/Python-2.7.5
make
make install
cd
rm -rf Python-2.7.5
Create a virtual environment¶
Create an isolated virtual environment where all your Python packages will be installed:
cd
cd CGAT
wget --no-check-certificate https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.10.1.tar.gz
tar xvfz virtualenv-1.10.1.tar.gz
rm virtualenv-1.10.1.tar.gz
cd virtualenv-1.10.1
$HOME/CGAT/Python-2.7.5/bin/python virtualenv.py cgat-venv
source cgat-venv/bin/activate
Install Python dependencies¶
Use pip to install all the packages on which CGAT Code Collection depends on:
pip install cython
pip install numpy
pip install pysam
pip install https://bitbucket.org/james_taylor/bx-python/get/tip.tar.bz2
pip install biopython
pip install pybedtools
pip install matplotlib
pip install scipy
pip install -r https://raw.github.com/CGATOxford/cgat/master/requires.txt
pip install CGAT
Test CGAT Code Collection¶
If everything went fine with the previous steps you should be able to execute the following command:
cgat --help
Finish the CGAT virtual environment¶
When you are done, you may deactivate the CGAT virtual environment:
deactivate
