|
3
|
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.
|
