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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
author peterjc
date Wed, 07 Oct 2015 10:31:49 -0400
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1 Galaxy wrapper for the MIRA assembly program (v4.9) mirabait
2 ============================================================
3
4 This tool is copyright 2011-2015 by Peter Cock, The James Hutton Institute
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
6 See the licence text below (MIT licence).
7
8 This is a Galaxy wrapper for ``mirabait`` from the MIRA 4.9 assembly suite.
9
10 It is available from the Galaxy Tool Shed at:
11 http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_9_mirabait
12
13 Development/test previews are available from the Galaxy Test Tool Shed at:
14 http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_9_mirabait
15
16 It is part of a suite for all the MIRA 4.9 tools:
17 TODO...
18
19 A separate wrapper for MIRA v4.0 is available from the Galaxy Tool Shed at:
20 http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
21
22
23 Automated Installation
24 ======================
25
26 This should be straightforward. Via the Tool Shed, Galaxy should automatically
27 install the precompiled binaries for MIRA v4.9.5, and offer to run any tests.
28
29
30 Manual Installation
31 ===================
32
33 There are various Python and XML files to install into Galaxy:
34
35 * ``mira4_9_mirabait.xml`` (the Galaxy tool definition for mirabait)
36 * ``mira_check_version.py`` (Python helper script)
37
38 The suggested location is a new ``tools/mira4_9`` folder. You will
39 also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
40 tool::
41
42 <tool file="mira4_9/mirabait/mira4_9_mirabait.xml" />
43 ...
44
45 You will also need to install MIRA 4.9, we used version 4.9.5, and define the
46 environment variable ``$MIRA4_9`` pointing at the folder containing the
47 binaries. See:
48
49 * http://chevreux.org/projects_mira.html
50 * http://sourceforge.net/projects/mira-assembler/
51
52 You may wish to use different cluster setups for the de novo and mapping
53 tools, see above.
54
55 You will also need to install samtools (for generating a BAM file from MIRA's
56 SAM output).
57
58 If you wish to run the unit tests, also move/copy the ``test-data/`` files
59 under Galaxy's ``test-data/`` folder. Then::
60
61 $ ./run_tests.sh -id mira4_9_mirabait
62 ...
63
64
65 History
66 =======
67
68 ======= ======================================================================
69 Version Changes
70 ------- ----------------------------------------------------------------------
71 v0.0.1 - Initial version for MIRA 4.9.5, based on wrapper for v4.0.2
72 ======= ======================================================================
73
74
75 Developers
76 ==========
77
78 Development is on a dedicated GitHub repository:
79 https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9
80
81 For pushing a release to the test or main "Galaxy Tool Shed", use the following
82 Planemo commands (which requires you have set your Tool Shed access details in
83 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
84
85 $ planemo shed_update -t testtoolshed --check_diff tools/mira4_9/
86 ...
87
88 or::
89
90 $ planemo shed_update -t toolshed --check_diff tools/mira4_9/
91 ...
92
93 To just build and check the tar ball, use::
94
95 $ planemo shed_upload --tar_only mira4_9/
96 ...
97 $ tar -tzf shed_upload.tar.gz
98 ...
99
100
101 Licence (MIT)
102 =============
103
104 Permission is hereby granted, free of charge, to any person obtaining a copy
105 of this software and associated documentation files (the "Software"), to deal
106 in the Software without restriction, including without limitation the rights
107 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
108 copies of the Software, and to permit persons to whom the Software is
109 furnished to do so, subject to the following conditions:
110
111 The above copyright notice and this permission notice shall be included in
112 all copies or substantial portions of the Software.
113
114 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
115 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
116 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
117 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
118 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
119 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
120 THE SOFTWARE.