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Uploaded kodoja_search.py v0.0.3 wrapper. https://github.com/abaizan/kodoja_galaxy/commit/55004d41a9c0750b2543f394594ee58cc4426609
author peterjc
date Wed, 14 Mar 2018 12:46:57 -0400
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1 .. image:: https://travis-ci.org/abaizan/kodoja_galaxy.svg?branch=master
2 :alt: Linux testing with TravisCI
3 :target: https://travis-ci.org/abaizan/kodoja_galaxy/branches
4
5 This is a Galaxy wrapper for the tool Kodoja, which is available to install in
6 conda from bioconda.
7
8 https://github.com/abaizan/kodoja
9
10 Galaxy wrappers for Kodoja
11 ==========================
12
13 These wrappers are copyright 2018 by Amanda Baizan Edge (University of
14 St Andrews, and The James Hutton Institute) and Peter Cock (The James
15 Hutton Institute). They are released under the MIT licence.
16
17 These wrappers are available from the Galaxy Tool Shed at:
18 http://toolshed.g2.bx.psu.edu/view/abaizan/kodoja
19
20 In-development test releases are available from the Test Tool Shed at:
21 http://testtoolshed.g2.bx.psu.edu/view/abaizan/kodoja
22
23
24 Citation
25 ========
26
27 Please refer to the main Kodoja citation instructions.
28
29
30 Automated Installation
31 ======================
32
33 Galaxy should be able to automatically install the dependencies, namely
34 ``kodoja`` and its dependencies like ``kraken`` and ``kaiju``, using the
35 conda and the bioconda recipes.
36
37 See the configuration notes below.
38
39
40 Configuration
41 =============
42
43 You must tell Galaxy about any Kraken and Kaiju databases using configuration
44 files ``kraken_databases.loc`` and ``kaiju_databases.loc`` which are located
45 in the ``tool-data/`` folder. Sample files are included which explain the
46 tab-based format to use.
47
48
49 History
50 =======
51
52 ======= ======================================================================
53 Version Changes
54 ------- ----------------------------------------------------------------------
55 v0.0.0 - Initial release covering ``kodoja_search.py`` v0.0.3.
56 ======= ======================================================================
57
58
59 Bug Reports
60 ===========
61
62 File a Galaxy wrapper issue at https://github.com/abaizan/kodoja_galaxy/issues
63
64 For issues with Kodoja itself, use https://github.com/abaizan/kodoja/issues
65
66
67 Developers
68 ==========
69
70 For pushing a release to the test or main "Galaxy Tool Shed", use the
71 following Planemo commands (which requires you have set your Tool Shed access
72 details in ``~/.planemo.yml`` and that you have access rights on the Tool
73 Shed)::
74
75 $ planemo shed_update -t testtoolshed --check_diff .
76 ...
77
78 or::
79
80 $ planemo shed_update -t toolshed --check_diff .
81 ...
82
83 To just build and check the tar ball, use::
84
85 $ planemo shed_upload -t testtoolshed --tar_only .
86 ...
87 $ tar -tzf shed_upload.tar.gz
88 LICENSE
89 README.rst
90 ...
91
92 This simplifies ensuring a consistent set of files is bundled each time,
93 including all the relevant test files.
94
95
96 Licence (MIT)
97 =============
98
99 Permission is hereby granted, free of charge, to any person obtaining a copy
100 of this software and associated documentation files (the "Software"), to deal
101 in the Software without restriction, including without limitation the rights
102 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
103 copies of the Software, and to permit persons to whom the Software is
104 furnished to do so, subject to the following conditions:
105
106 The above copyright notice and this permission notice shall be included in
107 all copies or substantial portions of the Software.
108
109 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
110 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
111 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
112 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
113 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
114 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
115 THE SOFTWARE.