|
0
|
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
|
|
1
|
48 For example, using https://doi.org/10.5281/zenodo.1406071 which is the
|
|
|
49 database provided with Kodoja::
|
|
|
50
|
|
|
51 $ cd /mnt/shared/data/
|
|
|
52 $ mkdir kodojaDB_v1.0
|
|
|
53 $ cd kodojaDB_v1.0
|
|
|
54 $ wget https://zenodo.org/record/1406071/files/kodojaDB_v1.0.tar.gz
|
|
|
55 $ tar -zxvf kodojaDB_v1.0.tar.gz
|
|
|
56
|
|
|
57 Then update your Galaxy configuration in ``tool-data/kraken_databases.loc``
|
|
|
58 to add a line like this::
|
|
|
59
|
|
|
60 kodojaDB_v1.0_kraken(tab)KodojaDB v1.0 (kraken), Sept 2018(tab)/mnt/shared/data/kodojaDB_v1.0/krakenDB
|
|
|
61
|
|
|
62 And likewise update ``tool-data/kaiju_databases.loc`` with a line like::
|
|
|
63
|
|
|
64 kodojaDB_v1.0_kaiju(tab)KodojaDB v1.0 (kaiju), Sept 2018(tab)/mnt/shared/data/kodojaDB_v1.0/kaijuDB
|
|
|
65
|
|
|
66 At the time of writing, reloading the ``*.loc`` files required restarting
|
|
|
67 the Galaxy server.
|
|
|
68
|
|
0
|
69
|
|
|
70 History
|
|
|
71 =======
|
|
|
72
|
|
|
73 ======= ======================================================================
|
|
|
74 Version Changes
|
|
|
75 ------- ----------------------------------------------------------------------
|
|
|
76 v0.0.0 - Initial release covering ``kodoja_search.py`` v0.0.3.
|
|
1
|
77 v0.0.4 - Minor update to call ``kodoja_search.py`` v0.0.4.
|
|
|
78 v0.0.6 - Minor update to call ``kodoja_search.py`` v0.0.6.
|
|
|
79 - Document installing the Kodoja databases from Zenodo.
|
|
0
|
80 ======= ======================================================================
|
|
|
81
|
|
|
82
|
|
|
83 Bug Reports
|
|
|
84 ===========
|
|
|
85
|
|
|
86 File a Galaxy wrapper issue at https://github.com/abaizan/kodoja_galaxy/issues
|
|
|
87
|
|
|
88 For issues with Kodoja itself, use https://github.com/abaizan/kodoja/issues
|
|
|
89
|
|
|
90
|
|
|
91 Developers
|
|
|
92 ==========
|
|
|
93
|
|
|
94 For pushing a release to the test or main "Galaxy Tool Shed", use the
|
|
|
95 following Planemo commands (which requires you have set your Tool Shed access
|
|
|
96 details in ``~/.planemo.yml`` and that you have access rights on the Tool
|
|
|
97 Shed)::
|
|
|
98
|
|
|
99 $ planemo shed_update -t testtoolshed --check_diff .
|
|
|
100 ...
|
|
|
101
|
|
|
102 or::
|
|
|
103
|
|
|
104 $ planemo shed_update -t toolshed --check_diff .
|
|
|
105 ...
|
|
|
106
|
|
|
107 To just build and check the tar ball, use::
|
|
|
108
|
|
|
109 $ planemo shed_upload -t testtoolshed --tar_only .
|
|
|
110 ...
|
|
|
111 $ tar -tzf shed_upload.tar.gz
|
|
|
112 LICENSE
|
|
|
113 README.rst
|
|
|
114 ...
|
|
|
115
|
|
|
116 This simplifies ensuring a consistent set of files is bundled each time,
|
|
|
117 including all the relevant test files.
|
|
|
118
|
|
|
119
|
|
|
120 Licence (MIT)
|
|
|
121 =============
|
|
|
122
|
|
|
123 Permission is hereby granted, free of charge, to any person obtaining a copy
|
|
|
124 of this software and associated documentation files (the "Software"), to deal
|
|
|
125 in the Software without restriction, including without limitation the rights
|
|
|
126 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
|
|
127 copies of the Software, and to permit persons to whom the Software is
|
|
|
128 furnished to do so, subject to the following conditions:
|
|
|
129
|
|
|
130 The above copyright notice and this permission notice shall be included in
|
|
|
131 all copies or substantial portions of the Software.
|
|
|
132
|
|
|
133 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
|
|
134 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
|
|
135 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
|
|
136 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
|
|
137 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
|
|
138 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
|
|
|
139 THE SOFTWARE.
|
