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comparison tools/mira3/README.rst @ 10:a2fb1e67bd11 draft

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Uploaded v0.0.9, correct path in dependency installation; renamed folder
author peterjc
date Thu, 30 Jan 2014 13:21:21 -0500
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1 Galaxy wrapper for the MIRA assembly program (v3.4)
2 ===================================================
3
4 This tool is copyright 2011-2013 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 convert MIRA's TCS file into a tab
10 separated file for use in Galaxy).
11
12 It is available from the Galaxy Tool Shed at:
13 http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
14
15
16 Automated Installation
17 ======================
18
19 This should be straightforward, Galaxy should automatically download and
20 install the precompiled binary for MIRA v3.4.0 for the Galaxy wrapper,
21 and run any tests.
22
23
24 Manual Installation
25 ===================
26
27 There are just two Galaxy files to install:
28
29 * mira.py (the Python script)
30 * mira.xml (the Galaxy tool definition)
31
32 The suggested location is a new tools/mira3 folder. You will also need to
33 modify the tools_conf.xml file to tell Galaxy to offer the tool, and also do
34 this to tools_conf.xml.sample in order to run any tests::
35
36 <tool file="mira3/mira.xml" />
37
38 You will also need to install MIRA, we used version 3.4.1.1. See:
39
40 * http://chevreux.org/projects_mira.html
41 * http://sourceforge.net/projects/mira-assembler/
42
43 WARNING: This tool was initially developed to construct viral genome assembly
44 and mapping pipelines, for which the run time and memory requirements are
45 negligible. For larger tasks, be aware that MIRA can require vast amounts
46 of RAM and run-times of over a week are possible. This tool wrapper makes
47 no attempt to spot and reject such large jobs.
48
49
50 History
51 =======
52
53 ======= ======================================================================
54 Version Changes
55 ------- ----------------------------------------------------------------------
56 v0.0.1 - Initial version (working prototype, using MIRA 3.2.1)
57 v0.0.2 - Improve capture of stdout/stderr (should see it as it runs)
58 v0.0.3 - Support Ion Torrent reads, now requires MIRA 3.4.0 or later
59 (some other switches changed, e.g. -OUT rrol to rrot, which
60 means the wrapper no longer works with MIRA 3.2.x)
61 - The contig summary file (TCS file) was removed in MIRA 3.4
62 - Report all missing output files (not just first missing one)
63 v0.0.4 - Fix problem with backbone arguments inroduced in v0.0.3
64 v0.0.5 - Implement the <version_command> tag to record the wrapper
65 version and the MIRA version being used.
66 - Check using MIRA 3.4 (later versions have a different API)
67 v0.0.6 - Tell MIRA to use /tmp for temporary files
68 - Tell MIRA to ignore long read names (otherwise it aborts)
69 v0.0.7 - Automated installation of the 64 bit Linux MIRA binary.
70 v0.0.8 - Basic unit test added (but commented out due to Galaxy issue).
71 - Link to Tool Shed added to help text and this documentation.
72 - Use reStructuredText for this README file.
73 - Adopted standard MIT licence.
74 - Updated citation information (Cock et al. 2013).
75 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
76 v0.0.9 - Renamed folder mira_assembler to mira3 (see also MIRA 4 wrapper).
77 - Correct path issue in automated dependency installation
78 ======= ======================================================================
79
80
81 Developers
82 ==========
83
84 This script and related tools were initially developed on the following hg branch:
85 http://bitbucket.org/peterjc/galaxy-central/src/tools
86
87 Development has now moved to a dedicated GitHub repository:
88 https://github.com/peterjc/pico_galaxy/tree/master/tools/mira_3_4
89
90 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
91 the following command from the Galaxy root folder::
92
93 $ tar -czf mira3_wrapper.tar.gz tools/mira3/README.rst tools/mira3/mira.xml tools/mira3/mira.py tools/mira3/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs.fasta
94
95 Check this worked::
96
97 $ tar -tzf mira3_wrapper.tar.gz
98 tools/mira3/README.rst
99 tools/mira3/mira.xml
100 tools/mira3/mira.py
101 tools/mira3/tool_dependencies.xml
102 test-data/tvc_mini.fastq
103 test-data/tvc_contigs.fasta
104
105
106 Licence (MIT)
107 =============
108
109 Permission is hereby granted, free of charge, to any person obtaining a copy
110 of this software and associated documentation files (the "Software"), to deal
111 in the Software without restriction, including without limitation the rights
112 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
113 copies of the Software, and to permit persons to whom the Software is
114 furnished to do so, subject to the following conditions:
115
116 The above copyright notice and this permission notice shall be included in
117 all copies or substantial portions of the Software.
118
119 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
120 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
121 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
122 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
123 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
124 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
125 THE SOFTWARE.