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annotate tools/mira4/README.rst @ 1:99fde64b9563 draft

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Uploaded v0.0.1 preview1, escape ampersand in XML
author peterjc
date Thu, 26 Sep 2013 12:25:21 -0400
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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 (MIT licence).
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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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15 Automated Installation
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16 ======================
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17
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18 This should be straightforward. Via the Tool Shed, Galaxy should automatically
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19 install the 'mira' datatype, download and install the precompiled binary for
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20 MIRA v4.0 for the Galaxy wrapper, and run any tests.
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21
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22 For MIRA 4, the Galaxy wrapper has been split in two, allowing separate
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23 cluster settings for de novo usage (high RAM) and mapping (lower RAM).
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24 Consult the Galaxy adminstration documentation for your cluster setup.
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25
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26 WARNING: This tool was developed to construct viral genome assembly and
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27 mapping pipelines, for which the run time and memory requirements are
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28 negligible. For larger tasks, be aware that MIRA can require vast amounts
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29 of RAM and run-times of over a week are possible. This tool wrapper makes
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30 no attempt to spot and reject such large jobs.
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32
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33 Manual Installation
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34 ===================
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35
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36 First install the 'mira' datatype for Galaxy, available here:
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37
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38 * http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes
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39
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40 There are just two Galaxy files to install:
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41
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42 * mira4.py (the Python script)
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43 * mira4_de_novo.xml (the Galaxy tool definition for de novo usage)
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44 * mira4_mapping.xml (the Galaxy tool definition for mapping usage)
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45
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46 The suggested location is a new tools/mira4 folder. You will also need to
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47 modify the tools_conf.xml file to tell Galaxy to offer the tool, and also do
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48 this to tools_conf.xml.sample in order to run any tests::
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49
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50 <tool file="mira4/mira4_de_novo.xml" />
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51 <tool file="mira4/mira4_mapping.xml" />
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52
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53 You will also need to install MIRA, we used version 4.0 RC2. See:
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54
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55 * http://chevreux.org/projects_mira.html
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56 * http://sourceforge.net/projects/mira-assembler/
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57
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58 You may wish to use different cluster setups for the de novo and mapping
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59 tools, see above.
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60
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61
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62 History
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63 =======
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64
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65 ======= ======================================================================
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66 Version Changes
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67 ------- ----------------------------------------------------------------------
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68 v0.0.1 - Initial version (prototype using MIRA 4.0 RC2, and wrapper for v3.4)
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69 ======= ======================================================================
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70
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71
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72 Developers
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73 ==========
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74
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75 Development is on a dedicated GitHub repository:
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76 https://github.com/peterjc/pico_galaxy/tree/master/tools/mira_4_0
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77
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78 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
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79 the following command from the Galaxy root folder::
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80
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81 $ 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/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs_mira4.fasta
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82
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83 Check this worked::
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84
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85 $ tar -tzf mira4_wrapper.tar.gz
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86 tools/mira4/README.rst
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87 tools/mira4/mira4_de_novo.xml
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88 tools/mira4/mira4_mapping.xml
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89 tools/mira4/mira4.py
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90 tools/mira4/tool_dependencies.xml
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91 test-data/tvc_mini.fastq
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92 test-data/tvc_contigs_mira4.fasta
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94
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95 Licence (MIT)
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96 =============
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97
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98 Permission is hereby granted, free of charge, to any person obtaining a copy
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99 of this software and associated documentation files (the "Software"), to deal
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100 in the Software without restriction, including without limitation the rights
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101 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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102 copies of the Software, and to permit persons to whom the Software is
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103 furnished to do so, subject to the following conditions:
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104
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105 The above copyright notice and this permission notice shall be included in
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106 all copies or substantial portions of the Software.
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107
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108 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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109 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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110 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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111 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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112 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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113 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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114 THE SOFTWARE.