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Update tool_dependencies to install package from pip
author Vimalkumar Velayudhan <vimal@biotechcoder.com>
date Mon, 31 Aug 2015 14:13:03 +0100
parents b78a5ba760b1
children 60bbd8ebe314
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17:805b779d4013 18:cff63cf0dea8
1 =============================== 1 ========
2 RiboPlot 2 RiboPlot
3 =============================== 3 ========
4 4
5 .. image:: https://img.shields.io/travis/vimalkumarvelayudhan/riboplot.svg 5 .. image:: https://img.shields.io/travis/vimalkumarvelayudhan/riboplot.svg
6 :target: https://travis-ci.org/vimalkumarvelayudhan/riboplot 6 :target: https://travis-ci.org/vimalkumarvelayudhan/riboplot
7 7
8 .. image:: https://img.shields.io/pypi/v/riboplot.svg 8 .. image:: https://img.shields.io/pypi/v/riboplot.svg
12 RiboPlot includes programs to plot and output Ribo-Seq read counts from an alignment file (BAM format). 12 RiboPlot includes programs to plot and output Ribo-Seq read counts from an alignment file (BAM format).
13 13
14 There are two programs in the package: 14 There are two programs in the package:
15 15
16 **riboplot** 16 **riboplot**
17
17 Plot and output read counts (csv) for a single transcript. 18 Plot and output read counts (csv) for a single transcript.
18 19
19 **ribocount** 20 **ribocount**
21
20 Output read counts for all transcripts in an alignment. 22 Output read counts for all transcripts in an alignment.
21 23
24 Free software: GPL license
22 25
23 Free software: GPL license. 26 Documentation: https://riboplot.readthedocs.org
24 27
25 Documentation: https://riboplot.readthedocs.org. 28 Repository: https://github.com/vimalkumarvelayudhan/riboplot
26 29
30 Requirements
31 ------------
32 Python packages
33 ...............
34 * matplotlib ``1.3.1``
35 * pysam ``0.8.3``
36
37 If you have a virtualenv setup, these packages and their dependencies can be installed
38 using::
39
40 pip install matplotlib==1.3.1
41 pip install pysam==0.8.3
42
43 Bedtools
44 ........
45 RNA coverage plot requires `bedtools <https://github.com/arq5x/bedtools2>`_ to be installed.
46
47 This release of riboplot has been tested with bedtools version ``2.17.0``.
48
49 On Ubuntu and derivatives, bedtools can be installed from the repositories using::
50
51 sudo apt-get install bedtools
52