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Uploaded v0.0.18, tweak display_data for running tests
author peterjc
date Mon, 25 Nov 2013 10:55:07 -0500
parents 7ceb2ae30ff4
children 939a600f45e9
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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 It is available from the Galaxy Tool Shed at:
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18 http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes
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19
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21 History
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22 =======
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23
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24 These versions numbers initially matched those for 'ncbi_blast_plus', but are
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25 not used explicitly in the datatypes themselves.
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26
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27 ======= ======================================================================
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28 Version Changes
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29 ------- ----------------------------------------------------------------------
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30 v0.0.11 - Final revision as part of the Galaxy main repository, and the
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31 first release via the Tool Shed
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32 v0.0.13 - Uses blast.py instead of xml.py to define the datatypes
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33 v0.0.14 - Includes datatypes for protein and nucleotide BLAST databases
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34 (based on work by Edward Kirton)
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35 v0.0.15 - Fixes a MetadataElement bug and includes more of the optional
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36 BLAST database files (contribution from Nicola Soranzo)
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37 v0.0.16 - Adopt standard MIT License.
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38 - Use reStructuredText for this README file.
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39 - Development moved to GitHub, https://github.com/peterjc/galaxy_blast
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40 - Nucleotide database definition aware of MegaBLAST index superheader
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41 v0.0.17 - Add maskinfo-asn1 and maskinfo-asn1-binary sub-datatypes
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42 v0.0.18 - Add retries to BLAST XML merge code.
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43 - Modify display_data method to allow unit tests to function.
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44 ======= ======================================================================
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46
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47 Installation
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48 ============
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49
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50 Doing this automatically via the Galaxy Tool Shed is probably simplest.
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53 Manual Installation
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54 ===================
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55
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56 Normally you would install this via the Galaxy ToolShed, which would move
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57 the provided blast.py file into a suitable location and process the
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58 datatypes_conf.xml entry to be combined with your local configuration.
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59
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60 However, if you really want to this should work for a manual install. Add
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61 the following lines to the datatypes_conf.xml file in the Galaxy main folder::
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62
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63 <datatype extension="blastxml" type="galaxy.datatypes.blast:BlastXml" mimetype="application/xml" display_in_upload="true"/>
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64 <datatype extension="blastdbn" type="galaxy.datatypes.blast:BlastNucDb" mimetype="text/html" display_in_upload="false"/>
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65 <datatype extension="blastdbp" type="galaxy.datatypes.blast:BlastProtDb" mimetype="text/html" display_in_upload="false"/>
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66
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67 and later in the sniffer section::
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68
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69 <sniffer type="galaxy.datatypes.blast:BlastXml"/>
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70
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71 Also create the file lib/galaxy/datatypes/blast.py by moving, copying or linking
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72 the blast.py file provided in this tar-ball. Finally add 'import blast' near
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73 the start of file lib/galaxy/datatypes/registry.py (after the other import
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74 lines).
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77 Bug Reports
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78 ===========
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79
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80 You can file an issue here https://github.com/peterjc/galaxy_blast/issues or ask
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81 us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev
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83
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84 Developers
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85 ==========
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86
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87 BLAST+ datatypes and wrappers, and other tools were originally developed on the
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88 following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools
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89
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90 As of July 2013, development is continuing on a dedicated GitHub repository:
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91 https://github.com/peterjc/galaxy_blast
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92
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93 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
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94 the following command from the blast_datatypes folder::
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95
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96 $ tar -czf blast_datatypes.tar.gz README.rst datatypes_conf.xml blast.py
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97
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98 Check this worked::
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99
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100 $ tar -tzf blast_datatypes.tar.gz
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101 README.rst
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102 datatypes_conf.xml
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103 blast.py
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104
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105 For development, rather than having a local ToolShed running, I currently
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106 use a symlink from lib/galaxy/datatypes/blast.py to the actual file as
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107 described above.
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108
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109
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110 Licence (MIT)
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111 =============
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112
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113 Permission is hereby granted, free of charge, to any person obtaining a copy
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114 of this software and associated documentation files (the "Software"), to deal
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115 in the Software without restriction, including without limitation the rights
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116 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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117 copies of the Software, and to permit persons to whom the Software is
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118 furnished to do so, subject to the following conditions:
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119
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120 The above copyright notice and this permission notice shall be included in
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121 all copies or substantial portions of the Software.
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122
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123 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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124 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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125 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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126 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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127 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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128 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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129 THE SOFTWARE.
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130
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131 NOTE: This is the licence for the Galaxy BLAST datatypes **only**. BLAST+
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132 and associated data files are available and licenced separately.