Mercurial > repos > peterjc > mira_assembler

annotate tools/mira_3_4/mira.txt @ 8:da604cc07658 draft

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Uploaded v0.0.8 take 2, adds links to Tool Shed.
author peterjc
date Thu, 02 May 2013 12:40:04 -0400
parents e810e45bdad7
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1 Galaxy tool to wrap the MIRA sequence assembly program (v3.4)
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2 =============================================================
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3
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4 This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute
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5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
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6 See the licence text below.
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7
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8 This tool is a short Python script (to collect the MIRA output and move it
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9 to where Galaxy expects the files, and convert MIRA's TCS file into a tab
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10 separated file for use in Galaxy).
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11
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12 It is available from the Galaxy Tool Shed at:
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13 http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
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16 Automated Installation
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17 ======================
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18
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19 This should be straightforward, Galaxy should automatically download and
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20 install the precompiled binary for MIRA v3.4.0 for the Galaxy wrapper,
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21 and run any tests.
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24 Manual Installation
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25 ===================
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26
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27 There are just two Galaxy files to install:
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28
c1c7d6f726b0 Uploaded v0.0.7 take 1, attempts automated installation of the MIRA binary.
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29 * mira.py (the Python script)
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30 * mira.xml (the Galaxy tool definition)
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31
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32 The suggested location is a new tools/mira_3_4 folder. You will also need to
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33 modify the tools_conf.xml file to tell Galaxy to offer the tool, and also do
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34 this to tools_conf.xml.sample in order to run any tests:
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35
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36 <tool file="mira_3_4/mira.xml" />
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37
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38 You will also need to install MIRA, we used version 3.4.1.1. See:
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39
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40 http://chevreux.org/projects_mira.html
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41 http://sourceforge.net/projects/mira-assembler/
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42
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43 WARNING: This tool was developed to construct viral genome assembly and
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44 mapping pipelines, for which the run time and memory requirements are
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45 negligible. For larger tasks, be aware that MIRA can require vast amounts
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46 of RAM and run-times of over a week are possible. This tool wrapper makes
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47 no attempt to spot and reject such large jobs.
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50 History
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51 =======
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52
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53 v0.0.1 - Initial version (working prototype, using MIRA 3.2.1)
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54 v0.0.2 - Improve capture of stdout/stderr (should see it as it runs)
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55 v0.0.3 - Support Ion Torrent reads, now requires MIRA 3.4.0 or later
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56 (some other switches changed, e.g. -OUT rrol to rrot, which
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57 means the wrapper no longer works with MIRA 3.2.x)
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58 - The contig summary file (TCS file) was removed in MIRA 3.4
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59 - Report all missing output files (not just first missing one)
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60 v0.0.4 - Fix problem with backbone arguments inroduced in v0.0.3
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61 v0.0.5 - Implement the <version_command> tag to record the wrapper
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62 version and the MIRA version being used.
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63 - Check using MIRA 3.4 (later versions have a different API)
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64 v0.0.6 - Tell MIRA to use /tmp for temporary files
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65 - Tell MIRA to ignore long read names (otherwise it aborts)
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66 v0.0.7 - Automated installation of the 64 bit Linux MIRA binary.
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67 v0.0.8 - Basic unit test added.
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68 - Link to Tool Shed added to help text and this documentation.
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71 Developers
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72 ==========
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73
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74 This script and related tools are being developed on the following hg branch:
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75 http://bitbucket.org/peterjc/galaxy-central/src/tools
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76
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77 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
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78 the following command from the Galaxy root folder:
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79
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80 $ tar -czf mira_wrapper.tar.gz tools/mira_3_4/mira.* tools/mira_3_4/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs.fasta
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81
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82 Check this worked:
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83
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84 $ tar -tzf mira_wrapper.tar.gz
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85 tools/mira_3_4/mira.py
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86 tools/mira_3_4/mira.txt
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87 tools/mira_3_4/mira.xml
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88 tools/mira_3_4/tool_dependencies.xml
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89 test-data/tvc_mini.fastq
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90 test-data/tvc_contigs.fasta
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92
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93 Licence (MIT/BSD style)
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94 =======================
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95
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96 Permission to use, copy, modify, and distribute this software and its
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97 documentation with or without modifications and for any purpose and
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98 without fee is hereby granted, provided that any copyright notices
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99 appear in all copies and that both those copyright notices and this
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100 permission notice appear in supporting documentation, and that the
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101 names of the contributors or copyright holders not be used in
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102 advertising or publicity pertaining to distribution of the software
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103 without specific prior permission.
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104
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105 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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106 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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107 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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108 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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109 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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110 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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111 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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112 OR PERFORMANCE OF THIS SOFTWARE.