Mercurial > repos > biotechcoder > riboseqr_wrapper
comparison README.rst @ 0:e01de823e919 draft default tip
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| author | biotechcoder |
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| date | Fri, 01 May 2015 05:41:51 -0400 |
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| -1:000000000000 | 0:e01de823e919 |
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| 1 README | |
| 2 ====== | |
| 3 | |
| 4 `riboSeqR <http://bioconductor.org/packages/release/bioc/html/riboSeqR.html>`_ | |
| 5 integration for `Galaxy <http://galaxyproject.org/>`_ / | |
| 6 `RiboGalaxy <http://ribogalaxy.ucc.ie/>`_. | |
| 7 | |
| 8 Included tools | |
| 9 -------------- | |
| 10 In the order in which they are run | |
| 11 | |
| 12 #. **Prepare riboSeqR Input** | |
| 13 | |
| 14 Prepare riboSeqR format input files from alignment files (SAM format, | |
| 15 Ribo-Seq or RNA-Seq alignments). | |
| 16 | |
| 17 #. **Triplet Periodicity** | |
| 18 | |
| 19 Plot triplet periodicity for different read lengths. | |
| 20 | |
| 21 #. **Metagene Analysis** | |
| 22 | |
| 23 Metagene analysis. | |
| 24 | |
| 25 #. **Plot Ribosome Profile** | |
| 26 | |
| 27 Plot Ribosome profile and output Ribo/RNA counts. | |
| 28 | |
| 29 Requirements | |
| 30 ------------ | |
| 31 * **R** (Tested with version ``3.2.0``). | |
| 32 | |
| 33 * **riboSeqR** (Tested with version ``1.0.4``). | |
| 34 | |
| 35 * **rpy2** Python module to interface with R. (Tested with version ``2.5.5``). | |
| 36 | |
| 37 Install R, riboSeqR, rpy2 on Ubuntu 14.04 | |
| 38 ......................................... | |
| 39 riboseqR requires recent R packages. Install R from CRAN mirror | |
| 40 (`instructions <http://cran.r-project.org/bin/linux/ubuntu/README>`_). | |
| 41 | |
| 42 In summary: | |
| 43 | |
| 44 Add to ``/etc/apt/sources.list`` :: | |
| 45 | |
| 46 deb http://ftp.heanet.ie/mirrors/cran.r-project.org/bin/linux/ubuntu trusty/ | |
| 47 | |
| 48 Install R:: | |
| 49 | |
| 50 sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 | |
| 51 sudo apt-get update | |
| 52 sudo apt-get install r-base r-base-dev | |
| 53 | |
| 54 To install riboSeqR R package:: | |
| 55 | |
| 56 sudo R | |
| 57 source("http://bioconductor.org/biocLite.R") | |
| 58 biocLite("riboSeqR") | |
| 59 | |
| 60 Install ``rpy2`` python module. Either using ``sudo``:: | |
| 61 | |
| 62 sudo apt-get install python-rpy2 | |
| 63 | |
| 64 or install in a virtualenv :: | |
| 65 | |
| 66 pip install rpy2 | |
| 67 | |
| 68 You can now install **riboseqr** from the toolshed. |