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Uploaded v0.0.16, moving to MIT license and development on GitHub. No functional changes.
author peterjc
date Mon, 29 Jul 2013 12:55:49 -0400
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1 Galaxy datatypes for NCBI BLAST+ suite
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2 ======================================
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3
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4 These Galaxy datatypes are copyright 2010-2013 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 Contributions/revisions copyright 2012 Edward Kirton. All rights reserved.
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7 Contributions/revisions copyright 2013 Nicola Soranzo. All rights reserved.
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8
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9 See the licence text below.
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10
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11 Note that these files (and the associated BLAST+ wrappers) were originally
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12 distributed as part of the main Galaxy repository, but as of August 2012 moved
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13 to the Galaxy Tool Shed as 'blast_datatypes' (and 'ncbi_blast_plus' for the
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14 wrappers). My thanks to Dannon Baker from the Galaxy development team for his
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15 assistance with this.
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16
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17
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18 History
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19 =======
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20
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21 These versions numbers initially matched those for 'ncbi_blast_plus', but are
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22 not used explicitly in the datatypes themselves.
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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 v0.0.11 - Final revision as part of the Galaxy main repository, and the
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28 first release via the Tool Shed
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29 v0.0.13 - Uses blast.py instead of xml.py to define the datatypes
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30 v0.0.14 - Includes datatypes for protein and nucleotide BLAST databases
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31 (based on work by Edward Kirton)
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32 v0.0.15 - Fixes a MetadataElement bug and includes more of the optional
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33 BLAST database files (contribution from Nicola Soranzo)
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34 v0.0.16 - Adopt standard MIT License.
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35 - Development moved to GitHub, https://github.com/peterjc/galaxy_blast
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36 ======= ======================================================================
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37
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38
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39 Installation
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40 ============
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41
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42 Doing this automatically via the Galaxy Tool Shed is probably simplest.
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44
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45 Manual Installation
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46 ===================
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47
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48 Normally you would install this via the Galaxy ToolShed, which would move
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49 the provided blast.py file into a suitable location and process the
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50 datatypes_conf.xml entry to be combined with your local configuration.
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51
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52 However, if you really want to this should work for a manual install. Add
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53 the following lines to the datatypes_conf.xml file in the Galaxy main folder::
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54
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55 <datatype extension="blastxml" type="galaxy.datatypes.blast:BlastXml" mimetype="application/xml" display_in_upload="true"/>
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56 <datatype extension="blastdbn" type="galaxy.datatypes.blast:BlastNucDb" mimetype="text/html" display_in_upload="false"/>
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57 <datatype extension="blastdbp" type="galaxy.datatypes.blast:BlastProtDb" mimetype="text/html" display_in_upload="false"/>
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58
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59 and later in the sniffer section::
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60
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61 <sniffer type="galaxy.datatypes.blast:BlastXml"/>
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62
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63 Also create the file lib/galaxy/datatypes/blast.py by moving, copying or linking
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64 the blast.py file provided in this tar-ball. Finally add 'import blast' near
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65 the start of file lib/galaxy/datatypes/registry.py (after the other import
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66 lines).
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67
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69 Bug Reports
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70 ===========
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71
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72 You can file an issue here https://github.com/peterjc/galaxy_blast/issues or ask
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73 us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev
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75
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76 Developers
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77 ==========
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78
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79 BLAST+ datatypes and wrappers, and other tools were originally developed on the
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80 following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools
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81
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82 As of July 2013, development is continuing on a dedicated GitHub repository:
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83 https://github.com/peterjc/galaxy_blast
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84
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85 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
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86 the following command from the blast_datatypes folder::
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87
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88 $ tar -czf blast_datatypes.tar.gz README.rst datatypes_conf.xml blast.py
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89
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90 Check this worked::
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91
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92 $ tar -tzf blast_datatypes.tar.gz
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93 README.rst
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94 datatypes_conf.xml
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95 blast.py
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96
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97 For development, rather than having a local ToolShed running, I currently
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98 use a symlink from lib/galaxy/datatypes/blast.py to the actual file as
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99 described above.
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100
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101
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102 Licence (MIT)
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103 =============
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104
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105 Permission is hereby granted, free of charge, to any person obtaining a copy
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106 of this software and associated documentation files (the "Software"), to deal
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107 in the Software without restriction, including without limitation the rights
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108 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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109 copies of the Software, and to permit persons to whom the Software is
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110 furnished to do so, subject to the following conditions:
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111
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112 The above copyright notice and this permission notice shall be included in
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113 all copies or substantial portions of the Software.
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114
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115 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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116 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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117 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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118 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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119 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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120 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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121 THE SOFTWARE.
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122
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123 NOTE: This is the licence for the Galaxy BLAST datatypes **only**. BLAST+
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124 and associated data files are available and licenced separately.