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Uploaded v0.0.8, MIT licence, RST for README, citation information, development moved to GitHub.
author peterjc
date Wed, 18 Sep 2013 06:22:19 -0400
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1 Galaxy tool to wrap the MIRA sequence 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/mira_3_4 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="mira_3_4/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 developed to construct viral genome assembly and
44 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 ======= ======================================================================
77
78
79 Developers
80 ==========
81
82 This script and related tools were initially developed on the following hg branch:
83 http://bitbucket.org/peterjc/galaxy-central/src/tools
84
85 Development has now moved to a dedicated GitHub repository:
86 https://github.com/peterjc/pico_galaxy/tree/master/tools/mira_3_4
87
88 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
89 the following command from the Galaxy root folder::
90
91 $ tar -czf mira_wrapper.tar.gz tools/mira_3_4/README.rst tools/mira_3_4/mira.xml tools/mira_3_4/mira.py tools/mira_3_4/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs.fasta
92
93 Check this worked::
94
95 $ tar -tzf mira_wrapper.tar.gz
96 tools/mira_3_4/README.rst
97 tools/mira_3_4/mira.xml
98 tools/mira_3_4/mira.py
99 tools/mira_3_4/tool_dependencies.xml
100 test-data/tvc_mini.fastq
101 test-data/tvc_contigs.fasta
102
103
104 Licence (MIT)
105 =============
106
107 Permission is hereby granted, free of charge, to any person obtaining a copy
108 of this software and associated documentation files (the "Software"), to deal
109 in the Software without restriction, including without limitation the rights
110 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
111 copies of the Software, and to permit persons to whom the Software is
112 furnished to do so, subject to the following conditions:
113
114 The above copyright notice and this permission notice shall be included in
115 all copies or substantial portions of the Software.
116
117 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
118 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
119 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
120 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
121 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
122 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
123 THE SOFTWARE.