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Uploaded v0.0.1, previously only on the Test Tool Shed
author peterjc
date Fri, 21 Nov 2014 06:38:46 -0500
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1 Galaxy datatypes for MIRA Assembly Format (MAF)
2 ===============================================
3
4 These Galaxy datatypes are copyright 2013 by Peter Cock, The James Hutton
5 Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
6
7 See the licence text below (MIT licence).
8
9 This code defines a 'mira' datatype within Galaxy for the MIRA Assembly Format
10 (specifically v2 of the format introduced by MIRA 4.0 and the development
11 preview releases of MIRA v3.9). See http://chevreux.org/projects_mira.html
12 and https://sourceforge.net/projects/mira-assembler/ for background.
13
14 This format is not to be confused with the existing 'maf' datatype within Galaxy
15 for the unrelated Multiple (sequence) Alignment Format (MAF).
16
17 It is available from the Galaxy Tool Shed at:
18 http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes
19
20
21 History
22 =======
23
24 ======= ======================================================================
25 Version Changes
26 ------- ----------------------------------------------------------------------
27 v0.0.1 - First public release
28 ======= ======================================================================
29
30
31 Installation
32 ============
33
34 Doing this automatically via the Galaxy Tool Shed is probably simplest, and will
35 happen automatically as a dependency of the Galaxy wrapper for MIRA v4.0.
36
37
38 Manual Installation
39 ===================
40
41 Normally you would install this via the Galaxy ToolShed, which would move
42 the provided mira.py file into a suitable location and process the
43 datatypes_conf.xml entry to be combined with your local configuration.
44
45 However, if you really want to this should work for a manual install. Add
46 the following lines to the datatypes_conf.xml file in the Galaxy main folder::
47
48 <datatype extension="mira" type="galaxy.datatypes.mira:MiraAssemblyFormat" mimetype="text/plain" display_in_upload="true"/>
49
50 and later in the sniffer section::
51
52 <sniffer type="galaxy.datatypes.mira:MiraAssemblyFormat"/>
53
54 Also create the file lib/galaxy/datatypes/mira.py by moving, copying or linking
55 the mira.py file provided in this tar-ball. Finally add 'import mira' near
56 the start of file lib/galaxy/datatypes/registry.py (after the other import
57 lines).
58
59
60 Bug Reports
61 ===========
62
63 You can file an issue here https://github.com/peterjc/pico_galaxy/issues or ask
64 us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev
65
66
67 Developers
68 ==========
69
70 Development is done on this GitHub repository:
71 https://github.com/peterjc/pico_galaxy
72
73 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
74 the following command from the mira_datatypes folder::
75
76 $ tar -czf mira_datatypes.tar.gz README.rst datatypes_conf.xml mira.py
77
78 Check this worked::
79
80 $ tar -tzf mira_datatypes.tar.gz
81 README.rst
82 datatypes_conf.xml
83 mira.py
84
85 For development, rather than having a local ToolShed running, I currently
86 use a symlink from lib/galaxy/datatypes/mira.py to the actual file as
87 described above.
88
89
90 Licence (MIT)
91 =============
92
93 Permission is hereby granted, free of charge, to any person obtaining a copy
94 of this software and associated documentation files (the "Software"), to deal
95 in the Software without restriction, including without limitation the rights
96 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
97 copies of the Software, and to permit persons to whom the Software is
98 furnished to do so, subject to the following conditions:
99
100 The above copyright notice and this permission notice shall be included in
101 all copies or substantial portions of the Software.
102
103 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
104 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
105 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
106 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
107 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
108 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
109 THE SOFTWARE.
110
111 NOTE: This is the licence for the Galaxy MIRA datatypes **only**. MIRA itself
112 is available and licenced separately.