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+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.