Mercurial > repos > devteam > blast_datatypes

annotate README.rst @ 8:de11e1a921c4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded v0.0.18, tweak display_data for running tests
author peterjc
date Tue, 21 Jan 2014 13:33:20 -0500
parents 5ec5dece43cb
children 2bda64d39931
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
1 Galaxy datatypes for NCBI BLAST+ suite
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
2 ======================================
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
3
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
4 These Galaxy datatypes are copyright 2010-2013 by Peter Cock, The James Hutton
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
5 Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
6 Contributions/revisions copyright 2012 Edward Kirton. All rights reserved.
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
7 Contributions/revisions copyright 2013 Nicola Soranzo. All rights reserved.
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
8
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
9 See the licence text below.
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
10
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
11 Note that these files (and the associated BLAST+ wrappers) were originally
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
12 distributed as part of the main Galaxy repository, but as of August 2012 moved
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
13 to the Galaxy Tool Shed as 'blast_datatypes' (and 'ncbi_blast_plus' for the
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
14 wrappers). My thanks to Dannon Baker from the Galaxy development team for his
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
15 assistance with this.
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
16
7
5ec5dece43cb Uploaded v0.0.17, Add maskinfo-asn1 and maskinfo-asn1-binary sub-datatypes
peterjc
parents: 6
diff changeset
17 It is available from the Galaxy Tool Shed at:
5ec5dece43cb Uploaded v0.0.17, Add maskinfo-asn1 and maskinfo-asn1-binary sub-datatypes
peterjc
parents: 6
diff changeset
18 http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes
5ec5dece43cb Uploaded v0.0.17, Add maskinfo-asn1 and maskinfo-asn1-binary sub-datatypes
peterjc
parents: 6
diff changeset
19
6
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
20
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
21 History
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
22 =======
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
23
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
24 These versions numbers initially matched those for 'ncbi_blast_plus', but are
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
25 not used explicitly in the datatypes themselves.
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
26
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
27 ======= ======================================================================
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
28 Version Changes
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
29 ------- ----------------------------------------------------------------------
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
30 v0.0.11 - Final revision as part of the Galaxy main repository, and the
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
31 first release via the Tool Shed
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
32 v0.0.13 - Uses blast.py instead of xml.py to define the datatypes
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
33 v0.0.14 - Includes datatypes for protein and nucleotide BLAST databases
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
34 (based on work by Edward Kirton)
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
35 v0.0.15 - Fixes a MetadataElement bug and includes more of the optional
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
36 BLAST database files (contribution from Nicola Soranzo)
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
37 v0.0.16 - Adopt standard MIT License.
7
5ec5dece43cb Uploaded v0.0.17, Add maskinfo-asn1 and maskinfo-asn1-binary sub-datatypes
peterjc
parents: 6
diff changeset
38 - Use reStructuredText for this README file.
6
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
39 - Development moved to GitHub, https://github.com/peterjc/galaxy_blast
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
40 - Nucleotide database definition aware of MegaBLAST index superheader
7
5ec5dece43cb Uploaded v0.0.17, Add maskinfo-asn1 and maskinfo-asn1-binary sub-datatypes
peterjc
parents: 6
diff changeset
41 v0.0.17 - Add maskinfo-asn1 and maskinfo-asn1-binary sub-datatypes
8
de11e1a921c4 Uploaded v0.0.18, tweak display_data for running tests
peterjc
parents: 7
diff changeset
42 v0.0.18 - Add retries to BLAST XML merge code.
de11e1a921c4 Uploaded v0.0.18, tweak display_data for running tests
peterjc
parents: 7
diff changeset
43 - Modify display_data method to allow unit tests to function.
6
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
44 ======= ======================================================================
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
45
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
46
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
47 Installation
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
48 ============
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
49
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
50 Doing this automatically via the Galaxy Tool Shed is probably simplest.
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
51
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
52
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
53 Manual Installation
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
54 ===================
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
55
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
56 Normally you would install this via the Galaxy ToolShed, which would move
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
57 the provided blast.py file into a suitable location and process the
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
58 datatypes_conf.xml entry to be combined with your local configuration.
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
59
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
60 However, if you really want to this should work for a manual install. Add
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
61 the following lines to the datatypes_conf.xml file in the Galaxy main folder::
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
62
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
63 <datatype extension="blastxml" type="galaxy.datatypes.blast:BlastXml" mimetype="application/xml" display_in_upload="true"/>
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
64 <datatype extension="blastdbn" type="galaxy.datatypes.blast:BlastNucDb" mimetype="text/html" display_in_upload="false"/>
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
65 <datatype extension="blastdbp" type="galaxy.datatypes.blast:BlastProtDb" mimetype="text/html" display_in_upload="false"/>
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
66
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
67 and later in the sniffer section::
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
68
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
69 <sniffer type="galaxy.datatypes.blast:BlastXml"/>
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
70
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
71 Also create the file lib/galaxy/datatypes/blast.py by moving, copying or linking
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
72 the blast.py file provided in this tar-ball. Finally add 'import blast' near
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
73 the start of file lib/galaxy/datatypes/registry.py (after the other import
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
74 lines).
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
75
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
76
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
77 Bug Reports
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
78 ===========
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
79
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
80 You can file an issue here https://github.com/peterjc/galaxy_blast/issues or ask
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
81 us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
82
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
83
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
84 Developers
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
85 ==========
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
86
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
87 BLAST+ datatypes and wrappers, and other tools were originally developed on the
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
88 following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
89
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
90 As of July 2013, development is continuing on a dedicated GitHub repository:
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
91 https://github.com/peterjc/galaxy_blast
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
92
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
93 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
94 the following command from the blast_datatypes folder::
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
95
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
96 $ tar -czf blast_datatypes.tar.gz README.rst datatypes_conf.xml blast.py
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
97
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
98 Check this worked::
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
99
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
100 $ tar -tzf blast_datatypes.tar.gz
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
101 README.rst
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
102 datatypes_conf.xml
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
103 blast.py
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
104
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
105 For development, rather than having a local ToolShed running, I currently
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
106 use a symlink from lib/galaxy/datatypes/blast.py to the actual file as
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
107 described above.
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
108
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
109
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
110 Licence (MIT)
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
111 =============
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
112
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
113 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
peterjc
parents:
diff changeset
114 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
peterjc
parents:
diff changeset
115 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
peterjc
parents:
diff changeset
116 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
peterjc
parents:
diff changeset
117 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
peterjc
parents:
diff changeset
118 furnished to do so, subject to the following conditions:
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
119
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
120 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
peterjc
parents:
diff changeset
121 all copies or substantial portions of the Software.
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
122
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
123 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
peterjc
parents:
diff changeset
124 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
peterjc
parents:
diff changeset
125 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
peterjc
parents:
diff changeset
126 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
peterjc
parents:
diff changeset
127 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
peterjc
parents:
diff changeset
128 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
peterjc
parents:
diff changeset
129 THE SOFTWARE.
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
130
a04cf51612f1 Uploaded v0.0.16, MIT License, development moved to GitHub, nucleotide database definition aware of MegaBLAST index superheader
peterjc
parents:
diff changeset
131 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
peterjc
parents:
diff changeset
132 and associated data files are available and licenced separately.