seqcluster 0.99.6

Small RNA-seq analysis

seqcluster
---------

small RNA analysis from NGS data

.. image:: https://travis-ci.org/lpantano/seqcluster.png?branch=master
:target: https://travis-ci.org/lpantano/seqcluster.png?branch=master

.. image:: https://badge.fury.io/py/seqcluster.svg
:target: http://badge.fury.io/py/seqcluster

.. image:: https://pypip.in/d/seqcluster/badge.png
:target: https://pypi.python.org/pypi/seqcluster


installation
---------

Install first bcbio-nextgen and cutadapter::

wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
bash Miniconda-latest-Linux-x86_64.sh -b -p ~/install/seqcluster/anaconda
PATH = ~/install/seqcluster/anaconda/bin:$PATH
conda install pip
conda install -c https://conda.binstar.org/bcbio bcbio-nextgen
pip install cutadapt

If you need to install bedtools, samtools and star::

git clone https://github.com/Homebrew/linuxbrew.git ~/install/seqcluster/linuxbrew
cd ~/install/seqcluster/linuxbrew/bin
ln -s `which gcc gcc-4.4`
PATH = ~/install/seqcluster/linuxbrew/bin:$PATH
brew tab homebrew/science
brew tab chapmanb/homebre-cbl
brew install bedtools
brew install samtools
brew install star-rna


Then you can get seqcluster::

pip install seqcluster

or the developement version::

git clone https://github.com/lpantano/seqcluster
cd seqcluster
python setup.py install