.. _install:

Installation
-------------

Requirements
~~~~~~~~~~~~

Xpression requires a UNIX-like environment, such as Linux or MacOSX and the following software:

Main software:

* Python 2.7
* bwa 0.5.7+
* samtools 0.1.10+

Python packages:

* pysam 0.3+
* Biopython 1.51+

GUI software:

* Java Runtime Environment (JRE) 1.5+

Install from package repository
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Many tools exist to acquire software packages quickly and easily. Simply browsing package managers like apt, yast and Fink will allow installation of what is needed without any lower-level steps.

Install from source
~~~~~~~~~~~~~~~~~~~~~

If a piece of software is not available as a package, you will need to install from source. Tools like :command:`gcc` and :command:`make` are needed to convert the text of the code into excutable software to run on your system. For MacOSX, this means XCode is needed, which includes Mac versions of those tools. 

For manual installation from source, the sequence of commands :command:`./configure`, :command:`make`, :command:`make install` are all that's needed. These steps can be automated with the installation script provided:

*   `Xpression_install.sh <https://bitbucket.org/clparallel/xpression.stable/src/tip/Xpression_install.sh>`_ 

This script downloads, compiles, and installs any software not found in the system's ``PATH``. It uses common system utilities and may require system-wide access priviledges, given by :command:`sudo`. It checks the system ``PATH`` for the software Xpression uses and, if found, verifies the minimum version number of that software is met.

To check the current installation state, run ``Xpression_install.sh`` with the ``-c`` option::

    $ sh Xpression_install.sh -c
    Checking for software needed for Xpression...
                Status
    BWA         installed.
    samtools    installed.
    python      installed.
    numpy       installed.
    Biopython   installed.
    pysam       not installed.
    Java        installed.

Here pysam needs to be installed before Xpression can run. 

Running the script again with the ``-i`` option will automatically retrieve and install what's needed.

Alternatives
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Xpression Virtual Environment
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

For those without a UNIX-like environment or from a non-technical background, we have provided a complete Linux environment that can be installed using freely-available software via a point-and-click process.

To use, first download and install software such as `VirtualBox <https://www.virtualbox.org/>`_ and follow their installation wizard. This software creates a virtual machine within the computer that can run images of any other system. Then download `Xpression VE <https://bitbucket.org/clparallel/xpression.stable/downloads/Xpression+RNAseq+analysis+pipeline.ova>`_ and follow :ref:`virtual` for instruction.

Amazon Web Services -- the `Cloud`
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

In the case of limited local resources, or for users wanting greater power or flexibility in their computing, an Amazon machine image is available at https://aws.amazon.com/amis/xpression-rna-seq-pipeline. This resource is currently not graphical, and must be accessed via the commandline. It contains the software used by Xpression as well as the latest version of Xpression itself, via mercurial. It is built directly on the Amazon Linux image, which is maintained and updated by the Amazon team to keep it secure and safe.