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annotate tools/mira4/README.rst @ 6:626d5cfd01aa draft

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Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
author peterjc
date Mon, 21 Oct 2013 12:01:47 -0400
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1 Galaxy wrapper for the MIRA assembly program (v4.0)
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2 ===================================================
0
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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 (MIT licence).
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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 associated Galaxy wrapper XML file.
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11 It is available from the Galaxy Tool Shed at:
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12 http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
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14 It uses a Galaxy datatype definition 'mira' for the MIRA Assembly Format,
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15 http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes
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16
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17 A separate wrapper for MIRA v3.4 is available from the Galaxy Tool Shed at:
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18 http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
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19
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20 Automated Installation
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21 ======================
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22
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23 This should be straightforward. Via the Tool Shed, Galaxy should automatically
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24 install the 'mira' datatype, download and install the precompiled binary for
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25 MIRA v4.0 for the Galaxy wrapper, and run any tests.
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26
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27 For MIRA 4, the Galaxy wrapper has been split in two, allowing separate
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28 cluster settings for de novo usage (high RAM) and mapping (lower RAM).
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29 Consult the Galaxy adminstration documentation for your cluster setup.
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31 WARNING: For larger tasks, be aware that MIRA can require vast amounts
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32 of RAM and run-times of over a week are possible. This tool wrapper makes
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33 no attempt to spot and reject such large jobs.
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34
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35
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36 Manual Installation
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37 ===================
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38
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39 First install the 'mira' datatype for Galaxy, available here:
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40
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41 * http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes
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42
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43 There are four Galaxy files to install:
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44
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45 * mira4.py (the Python wrapper script)
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46 * mira4_validator.py (the Python parameter validation script)
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47 * mira4_de_novo.xml (the Galaxy tool definition for de novo usage)
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48 * mira4_mapping.xml (the Galaxy tool definition for mapping usage)
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49
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50 The suggested location is a new tools/mira4 folder. You will also need to
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51 modify the tools_conf.xml file to tell Galaxy to offer the tool, and also do
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52 this to tools_conf.xml.sample in order to run any tests::
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53
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54 <tool file="mira4/mira4_de_novo.xml" />
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55 <tool file="mira4/mira4_mapping.xml" />
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56
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57 You will also need to install MIRA, we used version 4.0 RC4. See:
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58
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59 * http://chevreux.org/projects_mira.html
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60 * http://sourceforge.net/projects/mira-assembler/
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61
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62 You may wish to use different cluster setups for the de novo and mapping
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63 tools, see above.
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64
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65
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66 History
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67 =======
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68
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69 ======= ======================================================================
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70 Version Changes
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71 ------- ----------------------------------------------------------------------
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72 v0.0.1 - Initial version (prototype for MIRA 4.0 RC4, based on wrapper for v3.4)
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73 ======= ======================================================================
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74
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75
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76 Developers
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77 ==========
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78
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79 Development is on a dedicated GitHub repository:
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80 https://github.com/peterjc/pico_galaxy/tree/master/tools/mira4
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81
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82 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
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83 the following command from the Galaxy root folder::
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84
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85 $ tar -czf mira4_wrapper.tar.gz tools/mira4/README.rst tools/mira4/mira4_de_novo.xml tools/mira4/mira4_mapping.xml tools/mira4/mira4.py tools/mira4/mira4_validator.py tools/mira4/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs.fasta test-data/tvc_map_ref_strain.fasta test-data/tvc_map_same_strain.fasta
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86
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87 Check this worked::
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88
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89 $ tar -tzf mira4_wrapper.tar.gz
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90 tools/mira4/README.rst
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91 tools/mira4/mira4_de_novo.xml
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92 tools/mira4/mira4_mapping.xml
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93 tools/mira4/mira4.py
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94 tools/mira4/mira4_validator.py
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95 tools/mira4/tool_dependencies.xml
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96 test-data/tvc_mini.fastq
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97 test-data/tvc_contigs.fasta
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98 test-data/tvc_map_ref_strain.fasta
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99 test-data/tvc_map_same_strain.fasta
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101
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102 Licence (MIT)
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103 =============
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104
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105 Permission is hereby granted, free of charge, to any person obtaining a copy
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106 of this software and associated documentation files (the "Software"), to deal
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107 in the Software without restriction, including without limitation the rights
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108 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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109 copies of the Software, and to permit persons to whom the Software is
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110 furnished to do so, subject to the following conditions:
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111
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112 The above copyright notice and this permission notice shall be included in
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113 all copies or substantial portions of the Software.
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114
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115 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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116 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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117 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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118 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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119 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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120 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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diff changeset
121 THE SOFTWARE.