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Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
author peterjc
date Mon, 23 Sep 2013 09:56:10 -0400
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5:b3a3ba0c1d47 6:a04cf51612f1
1 Galaxy datatypes for NCBI BLAST+ suite
2 ======================================
3
4 These Galaxy datatypes are copyright 2010-2013 by Peter Cock, The James Hutton
5 Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
6 Contributions/revisions copyright 2012 Edward Kirton. All rights reserved.
7 Contributions/revisions copyright 2013 Nicola Soranzo. All rights reserved.
8
9 See the licence text below.
10
11 Note that these files (and the associated BLAST+ wrappers) were originally
12 distributed as part of the main Galaxy repository, but as of August 2012 moved
13 to the Galaxy Tool Shed as 'blast_datatypes' (and 'ncbi_blast_plus' for the
14 wrappers). My thanks to Dannon Baker from the Galaxy development team for his
15 assistance with this.
16
17
18 History
19 =======
20
21 These versions numbers initially matched those for 'ncbi_blast_plus', but are
22 not used explicitly in the datatypes themselves.
23
24 ======= ======================================================================
25 Version Changes
26 ------- ----------------------------------------------------------------------
27 v0.0.11 - Final revision as part of the Galaxy main repository, and the
28 first release via the Tool Shed
29 v0.0.13 - Uses blast.py instead of xml.py to define the datatypes
30 v0.0.14 - Includes datatypes for protein and nucleotide BLAST databases
31 (based on work by Edward Kirton)
32 v0.0.15 - Fixes a MetadataElement bug and includes more of the optional
33 BLAST database files (contribution from Nicola Soranzo)
34 v0.0.16 - Adopt standard MIT License.
35 - Development moved to GitHub, https://github.com/peterjc/galaxy_blast
36 - Nucleotide database definition aware of MegaBLAST index superheader
37 ======= ======================================================================
38
39
40 Installation
41 ============
42
43 Doing this automatically via the Galaxy Tool Shed is probably simplest.
44
45
46 Manual Installation
47 ===================
48
49 Normally you would install this via the Galaxy ToolShed, which would move
50 the provided blast.py file into a suitable location and process the
51 datatypes_conf.xml entry to be combined with your local configuration.
52
53 However, if you really want to this should work for a manual install. Add
54 the following lines to the datatypes_conf.xml file in the Galaxy main folder::
55
56 <datatype extension="blastxml" type="galaxy.datatypes.blast:BlastXml" mimetype="application/xml" display_in_upload="true"/>
57 <datatype extension="blastdbn" type="galaxy.datatypes.blast:BlastNucDb" mimetype="text/html" display_in_upload="false"/>
58 <datatype extension="blastdbp" type="galaxy.datatypes.blast:BlastProtDb" mimetype="text/html" display_in_upload="false"/>
59
60 and later in the sniffer section::
61
62 <sniffer type="galaxy.datatypes.blast:BlastXml"/>
63
64 Also create the file lib/galaxy/datatypes/blast.py by moving, copying or linking
65 the blast.py file provided in this tar-ball. Finally add 'import blast' near
66 the start of file lib/galaxy/datatypes/registry.py (after the other import
67 lines).
68
69
70 Bug Reports
71 ===========
72
73 You can file an issue here https://github.com/peterjc/galaxy_blast/issues or ask
74 us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev
75
76
77 Developers
78 ==========
79
80 BLAST+ datatypes and wrappers, and other tools were originally developed on the
81 following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools
82
83 As of July 2013, development is continuing on a dedicated GitHub repository:
84 https://github.com/peterjc/galaxy_blast
85
86 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
87 the following command from the blast_datatypes folder::
88
89 $ tar -czf blast_datatypes.tar.gz README.rst datatypes_conf.xml blast.py
90
91 Check this worked::
92
93 $ tar -tzf blast_datatypes.tar.gz
94 README.rst
95 datatypes_conf.xml
96 blast.py
97
98 For development, rather than having a local ToolShed running, I currently
99 use a symlink from lib/galaxy/datatypes/blast.py to the actual file as
100 described above.
101
102
103 Licence (MIT)
104 =============
105
106 Permission is hereby granted, free of charge, to any person obtaining a copy
107 of this software and associated documentation files (the "Software"), to deal
108 in the Software without restriction, including without limitation the rights
109 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
110 copies of the Software, and to permit persons to whom the Software is
111 furnished to do so, subject to the following conditions:
112
113 The above copyright notice and this permission notice shall be included in
114 all copies or substantial portions of the Software.
115
116 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
117 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
118 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
119 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
120 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
121 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
122 THE SOFTWARE.
123
124 NOTE: This is the licence for the Galaxy BLAST datatypes **only**. BLAST+
125 and associated data files are available and licenced separately.