Mercurial > repos > devteam > blast_datatypes
comparison blast_datatypes.txt @ 3:6ef523b390e0 draft
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author | peterjc |
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date | Thu, 20 Sep 2012 10:13:16 -0400 |
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children | f9a7783ed7b6 |
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1 Galaxy datatypes for NCBI BLAST+ suite | |
2 ====================================== | |
3 | |
4 These Galaxy datatypes are copyright 2010-2012 by Peter Cock, The James Hutton | |
5 Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. | |
6 See the licence text below. | |
7 | |
8 Note that these files (and the associated BLAST+ wrappers) were originally | |
9 distributed as part of the main Galaxy repository, but as of August 2012 moved | |
10 to the Galaxy Tool Shed as 'blast_datatypes' (and 'ncbi_blast_plus' for the | |
11 wrappers). My thanks to Dannon Baker from the Galaxy development team for his | |
12 assistance with this. | |
13 | |
14 | |
15 History | |
16 ======= | |
17 | |
18 These versions numbers match those for 'ncbi_blast_plus', but are not used | |
19 explicitly in the datatypes themselves. | |
20 | |
21 v0.0.11 - Final revision as part of the Galaxy main repository, and the | |
22 first release via the Tool Shed | |
23 v0.0.13 - Uses blast.py instead of xml.py to define the datatypes | |
24 | |
25 | |
26 Installation | |
27 ============ | |
28 | |
29 Doing this automatically via the Galaxy Tool Shed is probably simplest. | |
30 | |
31 | |
32 Manual Installation | |
33 =================== | |
34 | |
35 Normally you would install this via the Galaxy ToolShed, which would move | |
36 the provided blast.py file into a suitable location and process the | |
37 datatypes_conf.xml entry to be combined with your local configuration. | |
38 | |
39 However, if you really want to this should work for a manual install. Add | |
40 the following line to the datatypes_conf.xml file in the Galaxy main folder: | |
41 | |
42 <datatype extension="blastxml" type="galaxy.datatypes.blast:BlastXml" mimetype="application/xml" display_in_upload="true"/> | |
43 | |
44 Also create the file lib/galaxy/datatypes/blast.py by moving, copying or linking | |
45 the blast.py file provided in this tar-ball. Finally add 'import blast' near | |
46 the start of file lib/galaxy/datatypes/registry.py (after the other import | |
47 lines). | |
48 | |
49 | |
50 Developers | |
51 ========== | |
52 | |
53 BLAST+ datatypes and wrappers, and other tools are being developed on the | |
54 following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools | |
55 | |
56 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball I use | |
57 the following command from the Galaxy tools/ncbi_blast_plus folder: | |
58 | |
59 $ tar -czf blast_datatypes.tar.gz blast_datatypes.txt datatypes_conf.xml blast.py | |
60 | |
61 Check this worked: | |
62 | |
63 $ tar -tzf blast_datatypes.tar.gz | |
64 blast_datatypes.txt | |
65 datatypes_conf.xml | |
66 blast.py | |
67 | |
68 Note that the placement of these three files under tools/ncbi_blast_plus is | |
69 arbitrary - this just puts them next to the tool wrappers which use them. | |
70 | |
71 For development, rather than having a local ToolShed running, I currently | |
72 use a symlink from lib/galaxy/datatypes/blast.py to the actual file | |
73 tools/ncbi_blast_plus/blast.py as described above. | |
74 | |
75 | |
76 Licence (MIT/BSD style) | |
77 ======================= | |
78 | |
79 Permission to use, copy, modify, and distribute this software and its | |
80 documentation with or without modifications and for any purpose and | |
81 without fee is hereby granted, provided that any copyright notices | |
82 appear in all copies and that both those copyright notices and this | |
83 permission notice appear in supporting documentation, and that the | |
84 names of the contributors or copyright holders not be used in | |
85 advertising or publicity pertaining to distribution of the software | |
86 without specific prior permission. | |
87 | |
88 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL | |
89 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED | |
90 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE | |
91 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT | |
92 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS | |
93 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE | |
94 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE | |
95 OR PERFORMANCE OF THIS SOFTWARE. | |
96 | |
97 NOTE: This is the licence for the Galaxy BLAST datatypes only. BLAST+ | |
98 and associated data files are available and licenced separately. |