Installing seriesoftubes is easy if you already have Python and setuptools installed:
easy_install seriesoftubes
However, in order to use the scripts, you will need to manually install the external dependencies too.
seriesoftubes is written in and requires Python. Currently version >= 2.7 is required (Python 2.7.3 is recommended)
Setuptools (or distribute) is now required for installation. It is probably already installed, but if not, you must download and install it. It will install all the other python packages for you.
Several parts of seriesoftubes will not function properly on Windows, if at all. Mac OS X and Linux/*nix should work, and the pipeline has been most recently tested on Ubuntu 12.04 LTS.
If you install seriesoftubes using easy_install from setuptools (or an equivalent package), then it will automatically install most of the dependencies. If not, then you must install the following packages
Bowtie2 is used by align2.py (recommended) to align reads to the reference genome. Legacy support for bowtie is provided by align.py. align2.py expects bowtie2 to be in your PATH or in /usr/local/bowtie2(-*). Similarly, align.py expects bowtie to be in your PATH or in /usr/local/bowtie(-*).