Mercurial > repos > vimalkumarvelayudhan > riboplot
annotate README.rst @ 24:278d6aef2d7d
Attempt using a virtualenv
author | Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> |
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date | Tue, 01 Sep 2015 17:00:21 +0100 |
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1 ======== |
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2 RiboPlot |
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3 ======== |
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4 |
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5 .. image:: https://img.shields.io/travis/vimalkumarvelayudhan/riboplot.svg |
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6 :target: https://travis-ci.org/vimalkumarvelayudhan/riboplot |
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7 |
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8 .. image:: https://img.shields.io/pypi/v/riboplot.svg |
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9 :target: https://pypi.python.org/pypi/riboplot |
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10 |
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11 |
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12 RiboPlot includes programs to plot and output Ribo-Seq read counts from an alignment file (BAM format). |
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13 |
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14 There are two programs in the package: |
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16 **riboplot** |
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17 |
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18 Plot and output read counts (csv) for a single transcript. |
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19 |
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20 **ribocount** |
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22 Output read counts for all transcripts in an alignment. |
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23 |
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24 Free software: GPL license |
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26 Documentation: https://riboplot.readthedocs.org |
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28 Repository: https://github.com/vimalkumarvelayudhan/riboplot |
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30 Requirements |
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31 ------------ |
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32 Python packages |
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33 ............... |
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34 * matplotlib ``1.3.1`` |
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35 * pysam ``0.8.3`` |
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36 |
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37 If you have a virtualenv setup, these packages and their dependencies can be installed |
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38 using:: |
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39 |
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40 pip install matplotlib==1.3.1 |
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41 pip install pysam==0.8.3 |
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43 Bedtools |
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44 ........ |
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45 RNA coverage plot requires `bedtools <https://github.com/arq5x/bedtools2>`_ to be installed. |
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47 This release of riboplot has been tested with bedtools version ``2.17.0``. |
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48 |
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49 On Ubuntu and derivatives, bedtools can be installed from the repositories using:: |
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50 |
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51 sudo apt-get install bedtools |
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52 |