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comparison tools/mummer/README.rst @ 1:b07aa90c95e6 draft

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Uploaded v0.0.2, corrects typo on tool ID, adds citation markup.
author peterjc
date Tue, 28 Oct 2014 06:57:35 -0400
parents b0551f2a5986
children 8f93c1b7609e
comparison
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0:b0551f2a5986 1:b07aa90c95e6
1 Galaxy wrapper for EffectiveT3 v1.0.1 1 Galaxy wrapper for drawing dotplots using MUMmer 3
2 ===================================== 2 ==================================================
3 3
4 This wrapper is copyright 2014 by Peter Cock, The James Hutton Institute 4 This wrapper is copyright 2014 by Peter Cock, The James Hutton Institute
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. 5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
6 See the licence text below. 6 See the licence text below.
7 7
8 This is a wrapper for the command suite MUMmer v3. 8 This is a dotplot tool wrapping functionality from the MUMmer v3 suite.
9 9
10 S. Kurtz et al. (2004). 10 S. Kurtz et al. (2004).
11 Versatile and open software for comparing large genomes. 11 Versatile and open software for comparing large genomes.
12 Genome Biology (2004), 5:R12. 12 Genome Biology (2004), 5:R12.
13 http://dx.doi.org/10.1186/gb-2004-5-2-r12 13 http://dx.doi.org/10.1186/gb-2004-5-2-r12
19 ====================== 19 ======================
20 20
21 This should be straightforward, Galaxy should automatically download and install 21 This should be straightforward, Galaxy should automatically download and install
22 the MUMmer files. 22 the MUMmer files.
23 23
24 It also needs gnuplot, and ps2pdf. 24 It also needs the tools ``gnuplot`` and ``ps2pdf`` to be installed and on the
25 system ``$PATH``.
25 26
26 27
27 Manual Installation 28 Manual Installation
28 =================== 29 ===================
29 30
44 <tool file="mummer/mummer.xml" /> 45 <tool file="mummer/mummer.xml" />
45 46
46 If you wish to run the unit tests, also add this to ``tools_conf.xml.sample`` 47 If you wish to run the unit tests, also add this to ``tools_conf.xml.sample``
47 and move/copy the ``test-data`` files under Galaxy's ``test-data`` folder. Then:: 48 and move/copy the ``test-data`` files under Galaxy's ``test-data`` folder. Then::
48 49
49 $ ./run_functional_tests.sh -id mummer_wrapper 50 $ ./run_tests.sh -id mummerplot_wrapper
50 51
51 That's it. 52 That's it.
52 53
53 54
54 History 55 History
55 ======= 56 =======
56 57
57 ======= ====================================================================== 58 ======= ======================================================================
58 Version Changes 59 Version Changes
59 ------- ---------------------------------------------------------------------- 60 ------- ----------------------------------------------------------------------
60 v0.0.1 - Initial public release 61 v0.0.1 - Initial public release.
62 v0.0.2 - Correct typo in Tool identifier.
63 - Include MUMmer citation in Galaxy XML markup.
61 ======= ====================================================================== 64 ======= ======================================================================
62 65
63 66
64 Developers 67 Developers
65 ========== 68 ==========