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1 README
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2 ======
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3
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4 `riboSeqR <http://bioconductor.org/packages/release/bioc/html/riboSeqR.html>`_
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5 integration for `Galaxy <http://galaxyproject.org/>`_ /
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6 `RiboGalaxy <http://ribogalaxy.ucc.ie/>`_.
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7
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8 Included tools
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9 --------------
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10 In the order in which they are run
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11
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12 #. **Prepare riboSeqR Input**
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13
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14 Prepare riboSeqR format input files from alignment files (SAM format,
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15 Ribo-Seq or RNA-Seq alignments).
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16
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17 #. **Triplet Periodicity**
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18
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19 Plot triplet periodicity for different read lengths.
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20
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21 #. **Metagene Analysis**
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22
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23 Metagene analysis.
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24
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25 #. **Plot Ribosome Profile**
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26
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27 Plot Ribosome profile and output Ribo/RNA counts.
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28
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29 Requirements
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30 ------------
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31 * **R** (Tested with version ``3.2.0``).
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32
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33 * **riboSeqR** (Tested with version ``1.0.4``).
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34
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35 * **rpy2** Python module to interface with R. (Tested with version ``2.5.5``).
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36
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37 Install R, riboSeqR, rpy2 on Ubuntu 14.04
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38 .........................................
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39 riboseqR requires recent R packages. Install R from CRAN mirror
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40 (`instructions <http://cran.r-project.org/bin/linux/ubuntu/README>`_).
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41
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42 In summary:
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43
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44 Add to ``/etc/apt/sources.list`` ::
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45
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46 deb http://ftp.heanet.ie/mirrors/cran.r-project.org/bin/linux/ubuntu trusty/
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47
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48 Install R::
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49
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50 sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
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51 sudo apt-get update
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52 sudo apt-get install r-base r-base-dev
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53
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54 To install riboSeqR R package::
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55
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56 sudo R
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57 source("http://bioconductor.org/biocLite.R")
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58 biocLite("riboSeqR")
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59
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60 Install ``rpy2`` python module. Either using ``sudo``::
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61
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62 sudo apt-get install python-rpy2
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63
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64 or install in a virtualenv ::
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65
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66 pip install rpy2
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67
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68 You can now install **riboseqr** from the toolshed.
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