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