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annotate README.rst @ 12:da92fef90117 draft

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Uploaded v0.0.20 with new citation information
author peterjc
date Wed, 25 Feb 2015 10:50:44 -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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8 See the licence text below.
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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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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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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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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 ``blastdbd`` 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 v0.0.20 - Added "NCBI BLAST+ integrated into Galaxy" preprint citation.
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50 ======= ======================================================================
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53 Installation
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54 ============
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55
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56 Doing this automatically via the Galaxy Tool Shed is probably simplest.
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59 Manual Installation
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60 ===================
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61
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62 Normally you would install this via the Galaxy ToolShed, which would move
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63 the provided ``blast.py`` file into a suitable location and process the
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64 ``datatypes_conf.xml`` entries to be combined with your local configuration.
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65
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66 However, if you really want to this should work for a manual install. First
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67 update the ``datatypes_conf.xml`` file in the Galaxy main folder by inserting
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68 the contents of the ``<registration>`` and ``<sniffers>`` sections from the
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69 small ``datatypes_conf.xml`` file provided in the tar-ball.
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71 For the ``<registration>`` section you would add several ``<datatype ... />``
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72 lines, one per new datatype::
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74 <datatype extension="blastxml" type="galaxy.datatypes.blast:BlastXml" mimetype="application/xml" display_in_upload="true"/>
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75 ...
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76
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77 Similarly, some of the new dataypes have ``<sniffer ... />`` lines used to
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78 automatically recognise the datatype when uploaded into Galaxy::
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80 <sniffer type="galaxy.datatypes.blast:BlastXml"/>
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81 ...
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82
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83 Also create the file ``lib/galaxy/datatypes/blast.py`` by moving, copying or linking
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84 the ``blast.py`` file provided in this tar-ball. Finally add ``import blast`` near
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85 the start of file ``lib/galaxy/datatypes/registry.py`` (after the other import
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86 lines).
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89 Bug Reports
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90 ===========
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91
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92 You can file an issue here https://github.com/peterjc/galaxy_blast/issues or ask
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93 us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev
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96 Developers
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97 ==========
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98
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99 These BLAST+ datatypes and associated tools were originally developed on the
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100 following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools
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101
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102 As of July 2013, development is continuing on a dedicated GitHub repository:
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103 https://github.com/peterjc/galaxy_blast
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104
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105 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
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106 the following command from the ``blast_datatypes`` folder::
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107
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108 $ tar -czf blast_datatypes.tar.gz README.rst datatypes_conf.xml blast.py
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109
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110 Check this worked::
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111
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112 $ tar -tzf blast_datatypes.tar.gz
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113 README.rst
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114 datatypes_conf.xml
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115 blast.py
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116
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117 For development, rather than having a local ToolShed running, I currently
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118 use a symlink from ``lib/galaxy/datatypes/blast.py`` to the actual file as
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119 described above.
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121
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122 Citation
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123 ========
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124
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125 Please cite the following paper (currently available as a preprint):
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126
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127 NCBI BLAST+ integrated into Galaxy.
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128 P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo
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129 bioRxiv DOI: http://dx.doi.org/10.1101/014043 (preprint)
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130
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131
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132 Licence (MIT)
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133 =============
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134
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135 Permission is hereby granted, free of charge, to any person obtaining a copy
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136 of this software and associated documentation files (the "Software"), to deal
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137 in the Software without restriction, including without limitation the rights
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138 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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139 copies of the Software, and to permit persons to whom the Software is
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140 furnished to do so, subject to the following conditions:
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141
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142 The above copyright notice and this permission notice shall be included in
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143 all copies or substantial portions of the Software.
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144
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145 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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146 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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147 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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148 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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149 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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150 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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151 THE SOFTWARE.
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152
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153 NOTE: This is the licence for the Galaxy BLAST datatypes **only**. BLAST+
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154 and associated data files are available and licenced separately.