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Uploaded v0.0.4, previously only on the TestToolShed
author peterjc
date Fri, 21 Nov 2014 06:42:56 -0500
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1 Galaxy wrapper for the MIRA assembly program (v4.0)
2 ===================================================
3
4 This tool is copyright 2011-2014 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 four Galaxy files to install:
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`` folder. You will also need to
55 modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool, and also do
56 this to ``tools_conf.xml.sample`` in order to run the tests::
57
58 <tool file="mira4/mira4_de_novo.xml" />
59 <tool file="mira4/mira4_mapping.xml" />
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 After copying (or symlinking) the ``test-data`` files under Galaxy's ``test-data``
75 folder, you can run the tests with::
76
77 $ ./run_functional_tests.sh -id mira_4_0_bait
78 $ ./run_functional_tests.sh -id mira_4_0_de_novo
79 $ ./run_functional_tests.sh -id mira_4_0_mapping
80 $ ./run_functional_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 ======= ======================================================================
101
102
103 Developers
104 ==========
105
106 Development is on a dedicated GitHub repository:
107 https://github.com/peterjc/pico_galaxy/tree/master/tools/mira4
108
109 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
110 the following command from the Galaxy root folder::
111
112 $ tar -czf mira4_wrapper.tar.gz tools/mira4/README.rst tools/mira4/mira4_de_novo.xml tools/mira4/mira4_mapping.xml tools/mira4/mira4_bait.xml tools/mira4/mira4_convert.xml tools/mira4/mira4.py tools/mira4/mira4_make_bam.py tools/mira4/mira4_validator.py tools/mira4/mira4_convert.py tools/mira4/mira4_bait.py tools/mira4/tool_dependencies.xml tools/mira4/repository_dependencies.xml test-data/U13small_m.fastq test-data/U13small_m.mira4_de_novo.fasta test-data/tvc_mini.fastq test-data/tvc_contigs.fasta test-data/tvc_map_ref_strain.fasta test-data/tvc_map_same_strain.fasta test-data/tvc_bait.fasta test-data/tvc_mini_bait_pos.fastq test-data/tvc_mini_bait_strict.fastq test-data/tvc_mini_bait_neg.fastq test-data/ecoli.fastq test-data/ecoli.mira4_de_novo.fasta test-data/header.mira test-data/empty_file.dat
113
114 Check this worked::
115
116 $ tar -tzf mira4_wrapper.tar.gz
117 tools/mira4/README.rst
118 tools/mira4/mira4_de_novo.xml
119 tools/mira4/mira4_mapping.xml
120 tools/mira4/mira4_bait.xml
121 tools/mira4/mira4_convert.xml
122 tools/mira4/mira4.py
123 tools/mira4/mira4_make_bam.py
124 tools/mira4/mira4_validator.py
125 tools/mira4/mira4_convert.py
126 tools/mira4/mira4_bait.py
127 tools/mira4/tool_dependencies.xml
128 tools/mira4/repository_dependencies.xml
129 test-data/U13small_m.fastq
130 test-data/U13small_m.mira4_de_novo.fasta
131 test-data/tvc_mini.fastq
132 test-data/tvc_contigs.fasta
133 test-data/tvc_map_ref_strain.fasta
134 test-data/tvc_map_same_strain.fasta
135 test-data/tvc_bait.fasta
136 test-data/tvc_mini_bait_pos.fastq
137 test-data/tvc_mini_bait_strict.fastq
138 test-data/tvc_mini_bait_neg.fastq
139 test-data/ecoli.fastq
140 test-data/ecoli.mira4_de_novo.fasta
141 test-data/header.mira
142 test-data/empty_file.dat
143
144
145
146 Licence (MIT)
147 =============
148
149 Permission is hereby granted, free of charge, to any person obtaining a copy
150 of this software and associated documentation files (the "Software"), to deal
151 in the Software without restriction, including without limitation the rights
152 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
153 copies of the Software, and to permit persons to whom the Software is
154 furnished to do so, subject to the following conditions:
155
156 The above copyright notice and this permission notice shall be included in
157 all copies or substantial portions of the Software.
158
159 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
160 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
161 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
162 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
163 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
164 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
165 THE SOFTWARE.