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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 2010-2012 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 See the licence text below.
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7
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8 Note that these files (and the associated BLAST+ wrappers) were originally
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9 distributed as part of the main Galaxy repository, but as of August 2012 moved
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10 to the Galaxy Tool Shed as 'blast_datatypes' (and 'ncbi_blast_plus' for the
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11 wrappers). My thanks to Dannon Baker from the Galaxy development team for his
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12 assistance with this.
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13
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14
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15 History
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16 =======
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17
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18 These versions numbers match those for 'ncbi_blast_plus', but are not used
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19 explicitly in the datatypes themselves.
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20
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21 v0.0.11 - Final revision as part of the Galaxy main repository, and the
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22 first release via the Tool Shed
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23 v0.0.13 - Uses blast.py instead of xml.py to define the datatypes
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24 v0.0.14 - Includes datatypes for protein and nucleotide BLAST databases
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25 (based on work by Edward Kirton)
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3
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26
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27
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28 Installation
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29 ============
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30
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31 Doing this automatically via the Galaxy Tool Shed is probably simplest.
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32
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33
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34 Manual Installation
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35 ===================
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36
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37 Normally you would install this via the Galaxy ToolShed, which would move
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38 the provided blast.py file into a suitable location and process the
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39 datatypes_conf.xml entry to be combined with your local configuration.
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40
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41 However, if you really want to this should work for a manual install. Add
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42 the following lines to the datatypes_conf.xml file in the Galaxy main folder:
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43
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44 <datatype extension="blastxml" type="galaxy.datatypes.blast:BlastXml" mimetype="application/xml" display_in_upload="true"/>
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45 <datatype extension="blastdbn" type="galaxy.datatypes.blast:BlastNucDb" mimetype="text/html" display_in_upload="false"/>
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46 <datatype extension="blastdbp" type="galaxy.datatypes.blast:BlastProtDb" mimetype="text/html" display_in_upload="false"/>
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47
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48 and later in the sniffer section:
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49
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50 <sniffer type="galaxy.datatypes.blast:BlastXml"/>
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51
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52 Also create the file lib/galaxy/datatypes/blast.py by moving, copying or linking
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53 the blast.py file provided in this tar-ball. Finally add 'import blast' near
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54 the start of file lib/galaxy/datatypes/registry.py (after the other import
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55 lines).
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56
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57
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58 Developers
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59 ==========
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60
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61 BLAST+ datatypes and wrappers, and other tools are being developed on the
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62 following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools
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63
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64 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball I use
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65 the following command from the Galaxy tools/ncbi_blast_plus folder:
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66
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67 $ tar -czf blast_datatypes.tar.gz blast_datatypes.txt datatypes_conf.xml blast.py
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68
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69 Check this worked:
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70
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71 $ tar -tzf blast_datatypes.tar.gz
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72 blast_datatypes.txt
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73 datatypes_conf.xml
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74 blast.py
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75
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76 Note that the placement of these three files under tools/ncbi_blast_plus is
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77 arbitrary - this just puts them next to the tool wrappers which use them.
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78
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79 For development, rather than having a local ToolShed running, I currently
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80 use a symlink from lib/galaxy/datatypes/blast.py to the actual file
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81 tools/ncbi_blast_plus/blast.py as described above.
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82
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83
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84 Licence (MIT/BSD style)
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85 =======================
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86
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87 Permission to use, copy, modify, and distribute this software and its
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88 documentation with or without modifications and for any purpose and
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89 without fee is hereby granted, provided that any copyright notices
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90 appear in all copies and that both those copyright notices and this
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91 permission notice appear in supporting documentation, and that the
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92 names of the contributors or copyright holders not be used in
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93 advertising or publicity pertaining to distribution of the software
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94 without specific prior permission.
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95
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96 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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97 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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98 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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99 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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100 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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101 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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102 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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103 OR PERFORMANCE OF THIS SOFTWARE.
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104
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105 NOTE: This is the licence for the Galaxy BLAST datatypes only. BLAST+
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106 and associated data files are available and licenced separately.
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