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v0.0.8 - renamed folder, added note about mirabait
author peterjc
date Wed, 02 Sep 2015 07:46:29 -0400
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1 Galaxy wrapper for the MIRA assembly program (v4.0)
2 ===================================================
3
4 This tool is copyright 2011-2015 by Peter Cock, The James Hutton Institute
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
6 See the licence text below (MIT licence).
7
8 This tool is a short Python script (to collect the MIRA output and move it
9 to where Galaxy expects the files) and associated Galaxy wrapper XML file.
10
11 It is available from the Galaxy Tool Shed at:
12 http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
13
14 It uses a Galaxy datatype definition 'mira' for the MIRA Assembly Format,
15 http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes
16
17 A separate wrapper for MIRA v3.4 is available from the Galaxy Tool Shed at:
18 http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
19
20 Automated Installation
21 ======================
22
23 This should be straightforward. Via the Tool Shed, Galaxy should automatically
24 install the 'mira' datatype, samtools, and download and install the precompiled
25 binary for MIRA v4.0.2 for the Galaxy wrapper, and run any tests.
26
27 For MIRA 4, the Galaxy wrapper has been split in two, allowing separate
28 cluster settings for de novo usage (high RAM) and mapping (lower RAM).
29 Consult the Galaxy adminstration documentation for your cluster setup.
30
31 WARNING: For larger tasks, be aware that MIRA can require vast amounts
32 of RAM and run-times of over a week are possible. This tool wrapper makes
33 no attempt to spot and reject such large jobs.
34
35
36 Manual Installation
37 ===================
38
39 First install the 'mira' datatype for Galaxy, available here:
40
41 * http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes
42
43 There are various Python and XML files to install into Galaxy:
44
45 * ``mira4_de_novo.xml`` (the Galaxy tool definition for de novo usage)
46 * ``mira4_mapping.xml`` (the Galaxy tool definition for mapping usage)
47 * ``mira4_convert.xml`` (the Galaxy tool definition for converting MIRA files)
48 * ``mira4_bait.xml`` (the Galaxy tool definition for mirabait)
49 * ``mira4.py`` (the Python wrapper script)
50 * ``mira4_convert.py`` (the Python wrapper script for miraconvert)
51 * ``mira4_bait.py`` (the Python wrapper script for mirabait)
52 * ``mira4_validator.py`` (the XML parameter validation script)
53
54 The suggested location is a new ``tools/mira4_0`` folder. You will also need to
55 modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool::
56
57 <tool file="mira4_0/mira4_de_novo.xml" />
58 <tool file="mira4_0/mira4_mapping.xml" />
59 ...
60
61 You will also need to install MIRA, we used version 4.0.2, and define the
62 environment variable ``$MIRA4`` pointing at the folder containing the binaries.
63 See:
64
65 * http://chevreux.org/projects_mira.html
66 * http://sourceforge.net/projects/mira-assembler/
67
68 You may wish to use different cluster setups for the de novo and mapping
69 tools, see above.
70
71 You will also need to install samtools (for generating a BAM file from MIRA's
72 SAM output).
73
74 If you wish to run the unit tests, also move/copy the ``test-data/`` files
75 under Galaxy's ``test-data/`` folder. Then::
76
77 $ ./run_tests.sh -id mira_4_0_bait
78 $ ./run_tests.sh -id mira_4_0_de_novo
79 $ ./run_tests.sh -id mira_4_0_mapping
80 $ ./run_tests.sh -id mira_4_0_convert
81
82
83 History
84 =======
85
86 ======= ======================================================================
87 Version Changes
88 ------- ----------------------------------------------------------------------
89 v0.0.1 - Initial version (prototype for MIRA 4.0 RC4, based on wrapper for v3.4)
90 v0.0.2 - Include BAM output (using ``miraconvert`` and ``samtools``).
91 - Updated to target MIRA 4.0.1
92 - Simplified XML to apply input format to output data.
93 - Sets temporary folder at run time to respect environment variables
94 (``$TMPDIR``, ``$TEMP``, or ``$TMP`` in that order). This was
95 previously hard coded as ``/tmp``.
96 v0.0.3 - Updated to target MIRA 4.0.2
97 v0.0.4 - Using ``optparse`` for the Python wrapper script API
98 - Made MAF and BAM outputs optional
99 - Include wrapper for ``miraconvert``
100 v0.0.5 - Tool definition now embeds citation information.
101 v0.0.6 - Fixed error handling in ``mira4_convert.py``.
102 v0.0.7 - Renamed folder (internal change only).
103 - Reorder XML elements (internal change only).
104 - Use the ``format_source=...`` tag in the MIRA bait wrapper.
105 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
106 - MIRA 4.0.2 dependency now declared via dedicated Tool Shed package.
107 v0.0.8 - Renamed folder now have a MIRA 4.9.x wrapper (internal change only).
108 ======= ======================================================================
109
110
111 Developers
112 ==========
113
114 Development is on a dedicated GitHub repository:
115 https://github.com/peterjc/pico_galaxy/tree/master/tools/mira_4_0
116
117 For pushing a release to the test or main "Galaxy Tool Shed", use the following
118 Planemo commands (which requires you have set your Tool Shed access details in
119 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
120
121 $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/mira4_0/
122 ...
123
124 or::
125
126 $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/mira4_0/
127 ...
128
129 To just build and check the tar ball, use::
130
131 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/mira4_0/
132 ...
133 $ tar -tzf shed_upload.tar.gz
134 test-data/U13small_m.fastq
135 ...
136
137
138 Licence (MIT)
139 =============
140
141 Permission is hereby granted, free of charge, to any person obtaining a copy
142 of this software and associated documentation files (the "Software"), to deal
143 in the Software without restriction, including without limitation the rights
144 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
145 copies of the Software, and to permit persons to whom the Software is
146 furnished to do so, subject to the following conditions:
147
148 The above copyright notice and this permission notice shall be included in
149 all copies or substantial portions of the Software.
150
151 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
152 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
153 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
154 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
155 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
156 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
157 THE SOFTWARE.