Mercurial > repos > devteam > blast_datatypes
comparison README.rst @ 6:a04cf51612f1 draft
Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
author | peterjc |
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date | Mon, 23 Sep 2013 09:56:10 -0400 |
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children | 5ec5dece43cb |
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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. |