Mercurial > repos > peterjc > mira_assembler

annotate tools/mira3/README.rst @ 25:56dede4f0735 draft

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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira3/ commit 9526de68e38a82bb84b2d9267a8c290c6adcaa65
author peterjc
date Fri, 15 Sep 2017 10:08:39 -0400
parents 83a94a5038a7
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1 Galaxy wrapper for the MIRA assembly program (v3.4)
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2 ===================================================
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4 This tool is copyright 2011-2015 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 convert MIRA's TCS file into a tab
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10 separated file for use in Galaxy).
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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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19 This should be straightforward, Galaxy should automatically download and
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20 install the precompiled binary for MIRA v3.4.1.1 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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27 There are just two Galaxy files to install:
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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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32 The suggested location is a new ``tools/mira3`` folder. You will also need to
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33 modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool by adding
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34 the line::
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36 <tool file="mira3/mira.xml" />
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38 If you wish to run the unit tests, also move/copy the ``test-data/`` files
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39 under Galaxy's ``test-data/`` folder. Then::
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41 $ ./run_tests -id mira_assembler
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43 You will also need to install MIRA, we used version 3.4.1.1. See:
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45 * http://chevreux.org/projects_mira.html
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46 * http://sourceforge.net/projects/mira-assembler/
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48 WARNING: This tool was initially developed to construct viral genome assembly
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49 and mapping pipelines, for which the run time and memory requirements are
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50 negligible. For larger tasks, be aware that MIRA can require vast amounts
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51 of RAM and run-times of over a week are possible. This tool wrapper makes
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52 no attempt to spot and reject such large jobs.
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55 History
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56 =======
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58 ======= ======================================================================
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59 Version Changes
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60 ------- ----------------------------------------------------------------------
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61 v0.0.1 - Initial version (working prototype, using MIRA 3.2.1)
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62 v0.0.2 - Improve capture of stdout/stderr (should see it as it runs)
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63 v0.0.3 - Support Ion Torrent reads, now requires MIRA 3.4.0 or later
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64 (some other switches changed, e.g. -OUT rrol to rrot, which
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65 means the wrapper no longer works with MIRA 3.2.x)
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66 - The contig summary file (TCS file) was removed in MIRA 3.4
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67 - Report all missing output files (not just first missing one)
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68 v0.0.4 - Fix problem with backbone arguments inroduced in v0.0.3
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69 v0.0.5 - Implement the <version_command> tag to record the wrapper
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70 version and the MIRA version being used.
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71 - Check using MIRA 3.4 (later versions have a different API)
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72 v0.0.6 - Tell MIRA to use /tmp for temporary files
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73 - Tell MIRA to ignore long read names (otherwise it aborts)
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74 v0.0.7 - Automated installation of the 64 bit Linux MIRA binary.
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75 v0.0.8 - Basic unit test added (but commented out due to Galaxy issue).
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76 - Link to Tool Shed added to help text and this documentation.
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77 - Use reStructuredText for this README file.
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78 - Adopted standard MIT licence.
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79 - Updated citation information (Cock et al. 2013).
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80 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
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81 v0.0.9 - Renamed folder mira_assembler to mira3 (see also MIRA 4 wrapper).
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82 - Correct path issue in automated dependency installation.
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83 v0.0.10 - Added a functional test.
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84 - Updated URL for automated installation of MIRA v3.4.1.1
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85 v0.0.11 - Tool definition now embeds citation information.
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86 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
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87 - MIRA 3.4.1.1 dependency now declared via dedicated Tool Shed package.
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88 v0.0.12 - Python 3 compatible syntax (internal change only).
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89 - Use ``<command detect_errors="aggressive">`` (internal change only).
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90 - Single quote command line arguments (internal change only).
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91 ======= ======================================================================
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94 Developers
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95 ==========
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97 This script and related tools were initially developed on the following hg branch:
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98 http://bitbucket.org/peterjc/galaxy-central/src/tools
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99
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100 For some time developement continued at https://github.com/peterjc/pico_galaxy but
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101 is now in a dedicated GitHub repository: https://github.com/peterjc/galaxy_mira
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102
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103 For pushing a release to the test or main "Galaxy Tool Shed", use the following
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104 Planemo commands (which requires you have set your Tool Shed access details in
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105 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
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107 $ planemo shed_update -t testtoolshed --check_diff tools/mira3/
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108 ...
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109
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110 or::
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112 $ planemo shed_update -t toolshed --check_diff tools/mira3/
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113 ...
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114
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115 To just build and check the tar ball, use::
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117 $ planemo shed_upload --tar_only tools/mira3/
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118 ...
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119 $ tar -tzf shed_upload.tar.gz
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120 test-data/empty_file.dat
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121 test-data/tvc_contigs.fasta
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122 test-data/tvc_mini.fastq
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123 tools/mira3/README.rst
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124 tools/mira3/mira.py
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125 tools/mira3/mira.xml
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126 tools/mira3/tool_dependencies.xml
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127
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128
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129 Licence (MIT)
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130 =============
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131
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132 Permission is hereby granted, free of charge, to any person obtaining a copy
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133 of this software and associated documentation files (the "Software"), to deal
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134 in the Software without restriction, including without limitation the rights
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135 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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136 copies of the Software, and to permit persons to whom the Software is
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137 furnished to do so, subject to the following conditions:
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138
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139 The above copyright notice and this permission notice shall be included in
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140 all copies or substantial portions of the Software.
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141
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142 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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143 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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144 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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145 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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146 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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147 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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148 THE SOFTWARE.