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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
author galaxyp
date Thu, 11 Jan 2018 17:45:54 -0500
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1 Galaxy wrapper for OpenMS
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2 =========================
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4 OpenMS is an open-source software C++ library for LC/MS data management and analyses.
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5 It offers an infrastructure for the rapid development of mass spectrometry related software.
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6 OpenMS is free software available under the three clause BSD license and runs under Windows, MacOSX and Linux.
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8 More informations are available at:
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10 * https://github.com/OpenMS/OpenMS
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11 * http://open-ms.sourceforge.net
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14 Generating OpenMS wrappers
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15 ==========================
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17 * install OpenMS (you can do this automatically through Conda)
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18 * create a folder called CTD
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19 * if you installed openms as a binary in a specific directory, execute the following command in the `openms/bin` directory:
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21 ```bash
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22 for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done;
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23 ```
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25 * if there is no binary release (e.g. as with version 2.2), download and unpack the Conda package, find the `bin` folder and create a list of the tools as follow:
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27 ```bash
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28 ls >> tools.txt
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29 ```
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31 * search for the `bin` folder of your conda environment containing OpenMS and do:
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33 ```bash
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34 while read p; do
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35 ./PATH/TO/BIN/$p -write_ctd /PATH/TO/YOUR/CTD;
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36 done <tools.txt
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37 ```
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39 * You should have all CTD files now. `MetaProSIP.ctd` includes a not supported character: To use it, search for `²` and replace it (e.g. with `^2`).
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41 * clone or install CTDopts
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43 ```bash
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44 git clone https://github.com/genericworkflownodes/CTDopts
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45 ```
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47 * add CTDopts to your `$PYTHONPATH`
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49 ```bash
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50 export PYTHONPATH=/home/user/CTDopts/
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51 ```
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53 * clone or install CTD2Galaxy
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55 ```bash
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56 git clone https://github.com/WorkflowConversion/CTD2Galaxy.git
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57 ```
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59 * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. The default files are provided in this repository. You might have to install `libxslt` and `lxml` to run it.
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61 ```bash
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62 python generator.py \
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63 -i /PATH/TO/YOUR/CTD/*.ctd \
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64 -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \
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65 -d datatypes_conf.xml -g openms \
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66 -b version log debug test no_progress threads \
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67 in_type executable myrimatch_executable \
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68 fido_executable fidocp_executable \
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69 omssa_executable pepnovo_executable \
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70 xtandem_executable param_model_directory \
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71 java_executable java_memory java_permgen \
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72 r_executable rt_concat_trafo_out param_id_pool \
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73 -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \
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74 -s PATH/TO/SKIP_TOOLS_FILES.txt
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75 ```
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78 * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. For example:
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80 ```
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81 sed -i '13 a\-fido_executable Fido' wrappers/FidoAdapter.xml
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82 sed -i '13 a\-fidocp_executable FidoChooseParameters' wrappers/FidoAdapter.xml
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83 sed -i '13 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml
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84 sed -i '13 a\-omssa_executable omssa' wrappers/OMSSAAdapter.xml
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85 sed -i '13 a\-xtandem_executable xtandem' wrappers/XTandemAdapter.xml
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86 ```
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87
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88 * For some tools, additional work has to be done. In `MSGFPlusAdapter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where):
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89
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90 ```
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91 <command><![CDATA[
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92
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93 ## check input file type
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94 #set $in_type = $param_in.ext
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95
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96 ## create the symlinks to set the proper file extension, since msgf uses them to choose how to handle the input files
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97 ln -s '$param_in' 'param_in.${in_type}' &&
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98 ln -s '$param_database' param_database.fasta &&
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99 ## find location of the MSGFPlus.jar file of the msgf_plus conda package
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100 MSGF_JAR=\$(msgf_plus -get_jar_path) &&
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101
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102 MSGFPlusAdapter
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103 -executable \$MSGF_JAR
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104 #if $param_in:
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105 -in 'param_in.${in_type}'
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106 #end if
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107 #if $param_out:
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108 -out $param_out
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109 #end if
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110 #if $param_mzid_out:
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111 -mzid_out $param_mzid_out
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112 #end if
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113 #if $param_database:
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114 -database param_database.fasta
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115 #end if
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116
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117 [...]
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118 ]]>
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119 ```
6
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120
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121 * In Xtandem Converter and probably in others:
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122
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123 ```
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124 #if str($param_missed_cleavages) != '':
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125 ```
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126 This is because integers needs to be compared as string otherwise `0` becomes `false`.
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127
4
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128 * In `MetaProSIP.xml` add `R` as a requirement:
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129
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130 ```
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131 <expand macro="requirements">
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132 <requirement type="package" version="3.3.1">r-base</requirement>
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133 </expand>
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134 ```
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135
2
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136 * In `IDFileConverter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where):
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137
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138 ```
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139 <command><![CDATA[
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140
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141 ## check input file type
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142 #set $in_type = $param_in.ext
0
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143
2
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144 ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files
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145 ln -s '$param_in' 'param_in.${in_type}' &&
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146
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147 IDFileConverter
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148
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149 #if $param_in:
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150 -in 'param_in.${in_type}'
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151 #end if
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152
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153 [...]
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154 ]]>
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155 ```
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156
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157 * In `IDFileConverter.xml` and `FileConverter.xml` add `auto_format="true"` to the output, e.g.:
0
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158
2
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159 - `<data name="param_out" auto_format="true"/>`
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160 - `<data name="param_out" metadata_source="param_in" auto_format="true"/>`
0
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161
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162 * To add an example test case to `DecoyDatabase.xml` add the following after the output section. If standard settings change you might have to adjust the options and/or the test files.
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163
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164 ```
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165 <tests>
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166 <test>
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167 <param name="param_in" value="DecoyDatabase_input.fasta"/>
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168 <output name="param_out" file="DecoyDatabase_output.fasta"/>
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169 </test>
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170 </tests>
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171 ```
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172
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173
6
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174 * These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in
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175 by the automatic conversion step and are therefore in `SKIP_TOOLS_FILES.txt`:
0
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176 * SeedListGenerator
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177 * SpecLibSearcher
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178 * MapAlignerIdentification
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179 * MapAlignerPoseClustering
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180 * MapAlignerSpectrum
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181 * MapAlignerRTTransformer
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182
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183 * Additionally cause of lacking dependencies, the following adapters have been removed in `SKIP_TOOLS_FILES.txt` as well:
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184 * OMSSAAdapter
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185 * MyrimatchAdapter
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186
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187 * Additionally cause of a problematic parameter (-model_directory), the following adapter has been removed:
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188 * PepNovoAdapter
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189
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190
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191 Licence (MIT)
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192 =============
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193
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194 Permission is hereby granted, free of charge, to any person obtaining a copy
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195 of this software and associated documentation files (the "Software"), to deal
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196 in the Software without restriction, including without limitation the rights
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197 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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198 copies of the Software, and to permit persons to whom the Software is
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199 furnished to do so, subject to the following conditions:
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200
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201 The above copyright notice and this permission notice shall be included in
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202 all copies or substantial portions of the Software.
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203
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204 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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205 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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206 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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207 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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208 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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209 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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210 THE SOFTWARE.
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211