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1 Galaxy wrapper for the MIRA assembly program (v4.0)
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2 ===================================================
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3
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4 This tool is copyright 2011-2014 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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10
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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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13
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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, samtools, and download and install the precompiled
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25 binary for MIRA v4.0.2 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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30
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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_de_novo.xml`` (the Galaxy tool definition for de novo usage)
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46 * ``mira4_mapping.xml`` (the Galaxy tool definition for mapping usage)
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47 * ``mira4_convert.xml`` (the Galaxy tool definition for converting MIRA files)
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48 * ``mira4_bait.xml`` (the Galaxy tool definition for mirabait)
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49 * ``mira4.py`` (the Python wrapper script)
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50 * ``mira4_convert.py`` (the Python wrapper script for miraconvert)
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51 * ``mira4_bait.py`` (the Python wrapper script for mirabait)
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52 * ``mira4_validator.py`` (the XML parameter validation script)
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53
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54 The suggested location is a new ``tools/mira4`` folder. You will also need to
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55 modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool::
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56
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57 <tool file="mira4/mira4_de_novo.xml" />
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58 <tool file="mira4/mira4_mapping.xml" />
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59
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60 You will also need to install MIRA, we used version 4.0.2, and define the
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61 environment variable ``$MIRA4`` pointing at the folder containing the binaries.
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62 See:
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63
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64 * http://chevreux.org/projects_mira.html
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65 * http://sourceforge.net/projects/mira-assembler/
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66
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67 You may wish to use different cluster setups for the de novo and mapping
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68 tools, see above.
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69
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70 You will also need to install samtools (for generating a BAM file from MIRA's
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71 SAM output).
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72
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73 If you wish to run the unit tests, also move/copy the ``test-data/`` files
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74 under Galaxy's ``test-data/`` folder. Then::
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75
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76 $ ./run_tests.sh -id mira_4_0_bait
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77 $ ./run_tests.sh -id mira_4_0_de_novo
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78 $ ./run_tests.sh -id mira_4_0_mapping
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79 $ ./run_tests.sh -id mira_4_0_convert
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80
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81
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82 History
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83 =======
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84
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85 ======= ======================================================================
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86 Version Changes
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87 ------- ----------------------------------------------------------------------
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88 v0.0.1 - Initial version (prototype for MIRA 4.0 RC4, based on wrapper for v3.4)
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89 v0.0.2 - Include BAM output (using ``miraconvert`` and ``samtools``).
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90 - Updated to target MIRA 4.0.1
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91 - Simplified XML to apply input format to output data.
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92 - Sets temporary folder at run time to respect environment variables
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93 (``$TMPDIR``, ``$TEMP``, or ``$TMP`` in that order). This was
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94 previously hard coded as ``/tmp``.
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95 v0.0.3 - Updated to target MIRA 4.0.2
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96 v0.0.4 - Using ``optparse`` for the Python wrapper script API
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97 - Made MAF and BAM outputs optional
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98 - Include wrapper for ``miraconvert``
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99 v0.0.5 - Tool definition now embeds citation information.
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100 v0.0.6 - Fixed error handling in ``mira4_convert.py``.
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101 v0.0.7 - Renamed folder (internal change only).
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102 - Reorder XML elements (internal change only).
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103 - Use the ``format_source=...`` tag in the MIRA bait wrapper.
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104 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
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105 - MIRA 4.0.2 dependency now declared via dedicated Tool Shed package.
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106 ======= ======================================================================
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107
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108
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109 Developers
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110 ==========
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111
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112 Development is on a dedicated GitHub repository:
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113 https://github.com/peterjc/pico_galaxy/tree/master/tools/mira4_assembler
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114
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115 For pushing a release to the test or main "Galaxy Tool Shed", use the following
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116 Planemo commands (which requires you have set your Tool Shed access details in
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117 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
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118
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119 $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/mira4_assembler/
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120 ...
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121
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122 or::
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123
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124 $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/mira4_assembler/
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125 ...
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126
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127 To just build and check the tar ball, use::
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128
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129 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/mira4_assembler/
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130 ...
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131 $ tar -tzf shed_upload.tar.gz
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132 test-data/U13small_m.fastq
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133 test-data/U13small_m.mira4_de_novo.fasta
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134 test-data/ecoli.fastq
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135 test-data/ecoli.mira4_de_novo.fasta
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136 test-data/empty_file.dat
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137 test-data/header.mira
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138 test-data/tvc_mini.fastq
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139 test-data/tvc_contigs.fasta
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140 test-data/tvc_map_ref_strain.fasta
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141 test-data/tvc_map_same_strain.fasta
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142 test-data/tvc_bait.fasta
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143 test-data/tvc_mini_bait_neg.fastq
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144 test-data/tvc_mini_bait_pos.fastq
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145 test-data/tvc_mini_bait_strict.fastq
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146 tools/mira4_assembler/README.rst
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147 tools/mira4_assembler/mira4.py
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148 tools/mira4_assembler/mira4_bait.py
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149 tools/mira4_assembler/mira4_convert.py
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150 tools/mira4_assembler/mira4_de_novo.xml
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151 tools/mira4_assembler/mira4_make_bam.py
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152 tools/mira4_assembler/mira4_mapping.xml
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153 tools/mira4_assembler/mira4_validator.py
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154 tools/mira4_assembler/repository_dependencies.xml
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155 tools/mira4_assembler/tool_dependencies.xml
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156
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157
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158 Licence (MIT)
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159 =============
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160
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161 Permission is hereby granted, free of charge, to any person obtaining a copy
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162 of this software and associated documentation files (the "Software"), to deal
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163 in the Software without restriction, including without limitation the rights
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164 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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165 copies of the Software, and to permit persons to whom the Software is
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166 furnished to do so, subject to the following conditions:
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167
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168 The above copyright notice and this permission notice shall be included in
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169 all copies or substantial portions of the Software.
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170
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171 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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172 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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173 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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174 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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175 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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176 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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177 THE SOFTWARE.
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