README
======

`riboSeqR <http://bioconductor.org/packages/release/bioc/html/riboSeqR.html>`_
integration for `Galaxy <http://galaxyproject.org/>`_ /
`RiboGalaxy <http://ribogalaxy.ucc.ie/>`_.

Included tools
--------------
In the order in which they are run

#. **Prepare riboSeqR Input**

   Prepare riboSeqR format input files from alignment files (SAM format,
   Ribo-Seq or RNA-Seq alignments).

#. **Triplet Periodicity**

   Plot triplet periodicity for different read lengths.

#. **Metagene Analysis**

   Metagene analysis.

#. **Plot Ribosome Profile**

   Plot Ribosome profile and output Ribo/RNA counts.

Requirements
------------
* **R** (Tested with version ``3.2.0``).

* **riboSeqR** (Tested with version ``1.0.4``).

* **rpy2** Python module to interface with R. (Tested with version ``2.5.5``).

Install R, riboSeqR, rpy2 on Ubuntu 14.04
.........................................
riboseqR requires recent R packages. Install R from CRAN mirror
(`instructions <http://cran.r-project.org/bin/linux/ubuntu/README>`_).

In summary:

Add to ``/etc/apt/sources.list`` ::

    deb http://ftp.heanet.ie/mirrors/cran.r-project.org/bin/linux/ubuntu trusty/

Install R::

    sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
    sudo apt-get update
    sudo apt-get install r-base r-base-dev

To install riboSeqR R package::

    sudo R
    source("http://bioconductor.org/biocLite.R")
    biocLite("riboSeqR")

Install ``rpy2`` python module. Either using ``sudo``::

    sudo apt-get install python-rpy2

or install in a virtualenv ::

    pip install rpy2

You can now install **riboseqr** from the toolshed.