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Uploaded v0.0.19, adds blastdbp and pssm-asn1 datatypes.
author peterjc
date Wed, 26 Nov 2014 06:55:48 -0500
parents de11e1a921c4
children 5482a8cd0f36
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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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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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20 History
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21 =======
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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 ``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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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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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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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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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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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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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
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
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124 Permission is hereby granted, free of charge, to any person obtaining a copy
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
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125 of this software and associated documentation files (the "Software"), to deal
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
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126 in the Software without restriction, including without limitation the rights
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
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127 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
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128 copies of the Software, and to permit persons to whom the Software is
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
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129 furnished to do so, subject to the following conditions:
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130
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
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131 The above copyright notice and this permission notice shall be included in
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
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132 all copies or substantial portions of the Software.
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133
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
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134 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
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135 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
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136 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
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137 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
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138 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
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139 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
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140 THE SOFTWARE.
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
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141
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
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142 NOTE: This is the licence for the Galaxy BLAST datatypes **only**. BLAST+
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
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143 and associated data files are available and licenced separately.