annotate README.rst @ 24:278d6aef2d7d

Attempt using a virtualenv
author Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
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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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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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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12 RiboPlot includes programs to plot and output Ribo-Seq read counts from an alignment file (BAM format).
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14 There are two programs in the package:
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16 **riboplot**
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18 Plot and output read counts (csv) for a single transcript.
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20 **ribocount**
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22 Output read counts for all transcripts in an alignment.
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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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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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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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49 On Ubuntu and derivatives, bedtools can be installed from the repositories using::
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51 sudo apt-get install bedtools
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