Mercurial > repos > devteam > blast_datatypes
annotate README.rst @ 9:2bda64d39931 draft
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author | peterjc |
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date | Wed, 26 Nov 2014 06:55:48 -0500 |
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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 2010-2014 by Peter Cock (The James Hutton |
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5 Institute, UK) and additional contributors including Edward Kirton, Nicola |
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6 Soranzo, and Bjoern Gruening. |
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7 |
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8 See the licence text below. |
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9 |
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10 Note that these files (and the associated BLAST+ wrappers) were originally |
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11 distributed as part of the main Galaxy repository, but as of August 2012 moved |
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12 to the Galaxy Tool Shed as 'blast_datatypes' (and 'ncbi_blast_plus' for the |
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13 wrappers). My thanks to Dannon Baker from the Galaxy development team for his |
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14 assistance with this. |
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15 |
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16 It is available from the Galaxy Tool Shed at: |
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17 http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes |
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18 |
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19 |
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20 History |
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21 ======= |
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22 |
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23 These versions numbers initially matched those for 'ncbi_blast_plus', but are |
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24 not used explicitly in the datatypes themselves. |
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25 |
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26 ======= ====================================================================== |
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27 Version Changes |
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28 ------- ---------------------------------------------------------------------- |
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29 v0.0.11 - Final revision as part of the Galaxy main repository, and the |
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30 first release via the Tool Shed |
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31 v0.0.13 - Uses ``blast.py`` instead of ``xml.py`` to define the datatypes |
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32 v0.0.14 - Includes datatypes for protein and nucleotide BLAST databases |
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33 (``blastdbp`` and ``blastdbn``, based on work by Edward Kirton) |
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34 v0.0.15 - Fixes a MetadataElement bug and includes more of the optional |
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35 BLAST database files (contribution from Nicola Soranzo) |
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36 v0.0.16 - Adopt standard MIT License. |
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37 - Use reStructuredText for this README file. |
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38 - Development moved to GitHub, https://github.com/peterjc/galaxy_blast |
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39 - Nucleotide database definition aware of MegaBLAST index superheader |
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40 v0.0.17 - Add ``maskinfo-asn1`` and ``maskinfo-asn1-binary`` sub-datatypes |
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41 (contribution from Nicola Soranzo) |
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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 v0.0.19 - Add ``blastdbp`` datatype for BLAST protein domain databases, for use |
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45 with makeprofiledb and rpsblast (contribution from Bjoern Gruening). |
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46 - Add ``pssm-asn1`` datatype for Position Specific Scoring Matrices |
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47 (PSSMs) stored in NCBI's "scoremat" ASN.1 format (usually named |
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48 as *.smp), used as input files for makeprofiledb. |
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49 ======= ====================================================================== |
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50 |
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51 |
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52 Installation |
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53 ============ |
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54 |
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55 Doing this automatically via the Galaxy Tool Shed is probably simplest. |
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56 |
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57 |
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58 Manual Installation |
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59 =================== |
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60 |
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61 Normally you would install this via the Galaxy ToolShed, which would move |
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62 the provided ``blast.py`` file into a suitable location and process the |
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63 ``datatypes_conf.xml`` entries to be combined with your local configuration. |
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64 |
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65 However, if you really want to this should work for a manual install. First |
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66 update the ``datatypes_conf.xml`` file in the Galaxy main folder by inserting |
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67 the contents of the ``<registration>`` and ``<sniffers>`` sections from the |
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68 small ``datatypes_conf.xml`` file provided in the tar-ball. |
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69 |
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70 For the ``<registration>`` section you would add several ``<datatype ... />`` |
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71 lines, one per new datatype:: |
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72 |
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73 <datatype extension="blastxml" type="galaxy.datatypes.blast:BlastXml" mimetype="application/xml" display_in_upload="true"/> |
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74 ... |
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75 |
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76 Similarly, some of the new dataypes have ``<sniffer ... />`` lines used to |
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77 automatically recognise the datatype when uploaded into Galaxy:: |
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78 |
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79 <sniffer type="galaxy.datatypes.blast:BlastXml"/> |
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80 ... |
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81 |
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82 Also create the file ``lib/galaxy/datatypes/blast.py`` by moving, copying or linking |
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83 the ``blast.py`` file provided in this tar-ball. Finally add ``import blast`` near |
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84 the start of file ``lib/galaxy/datatypes/registry.py`` (after the other import |
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85 lines). |
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86 |
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87 |
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88 Bug Reports |
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89 =========== |
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90 |
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91 You can file an issue here https://github.com/peterjc/galaxy_blast/issues or ask |
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92 us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev |
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93 |
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94 |
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95 Developers |
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96 ========== |
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97 |
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98 These BLAST+ datatypes and associated tools were originally developed on the |
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99 following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools |
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100 |
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101 As of July 2013, development is continuing on a dedicated GitHub repository: |
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102 https://github.com/peterjc/galaxy_blast |
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103 |
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104 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use |
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105 the following command from the ``blast_datatypes`` folder:: |
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106 |
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107 $ tar -czf blast_datatypes.tar.gz README.rst datatypes_conf.xml blast.py |
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108 |
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109 Check this worked:: |
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110 |
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111 $ tar -tzf blast_datatypes.tar.gz |
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112 README.rst |
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113 datatypes_conf.xml |
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114 blast.py |
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115 |
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116 For development, rather than having a local ToolShed running, I currently |
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117 use a symlink from ``lib/galaxy/datatypes/blast.py`` to the actual file as |
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118 described above. |
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119 |
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120 |
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121 Licence (MIT) |
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122 ============= |
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123 |
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124 Permission is hereby granted, free of charge, to any person obtaining a copy |
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125 of this software and associated documentation files (the "Software"), to deal |
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126 in the Software without restriction, including without limitation the rights |
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127 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
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128 copies of the Software, and to permit persons to whom the Software is |
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129 furnished to do so, subject to the following conditions: |
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130 |
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131 The above copyright notice and this permission notice shall be included in |
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132 all copies or substantial portions of the Software. |
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133 |
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134 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR |
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135 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, |
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136 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE |
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137 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER |
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138 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, |
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139 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN |
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140 THE SOFTWARE. |
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141 |
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142 NOTE: This is the licence for the Galaxy BLAST datatypes **only**. BLAST+ |
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143 and associated data files are available and licenced separately. |