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annotate tool_dependencies.xml @ 9:9f30de0ff090 draft

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Add gmap_setup_bin and gmap_index_directory to defuse.xml config file generation
author Jim Johnson <jj@umn.edu>
date Mon, 14 Jan 2013 11:26:17 -0600
parents 1ea6445491d4
children b22f8634ff84
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="defuse" version="0.6.0">
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4 <install version="1.0">
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5 <actions>
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6 <action type="download_by_url">http://sourceforge.net/projects/defuse/files/defuse/0.6/defuse-0.6.0.tar.gz</action>
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7 <action type="shell_command">cd tools &amp;&amp; make</action>
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8 <action type="move_directory_files">
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9 <source_directory>.</source_directory>
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10 <destination_directory>$INSTALL_DIR</destination_directory>
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11 </action>
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12 <action type="set_environment">
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13 <environment_variable name="DEFUSE_PATH" action="set_to">$INSTALL_DIR</environment_variable>
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14 </action>
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15 </actions>
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16 </install>
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17 <readme>
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18 deFuse code
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19 To build the deFuse toolset you must have the boost c++ development libraries installed. If they are not installed on your system you can download them from the boost website. A full install of boost is not required. The easiest thing to do is to download the latest boost source tar.gz, extract it, then add the extracted path to the CPLUS_INCLUDE_PATH environment variable (in bash, `export CPLUS_INCLUDE_PATH=/boost/directory/:$CPLUS_INCLUDE_PATH`)
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20 </readme>
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21 </package>
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22
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23 <package name="samtools" version="0.1.18">
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24 <install version="1.0">
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25 <actions>
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26 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
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27 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
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28 <action type="shell_command">make</action>
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29 <action type="move_file">
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30 <source>samtools</source>
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31 <destination>$INSTALL_DIR/bin</destination>
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32 </action>
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33 <action type="move_file">
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34 <source>misc/maq2sam-long</source>
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35 <destination>$INSTALL_DIR/bin</destination>
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36 </action>
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37 <action type="set_environment">
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38 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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39 </action>
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40 </actions>
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41 </install>
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42 <readme>
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43 Compiling SAMtools requires the ncurses and zlib development libraries.
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44 </readme>
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45 </package>
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46
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47
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48 <package name="bowtie" version="0.12.7">
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49 <install version="1.0">
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50 <actions>
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51 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.7/bowtie-0.12.7-src.zip</action>
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52 <action type="shell_command">make</action>
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53 <action type="move_file">
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54 <source>bowtie</source>
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55 <destination>$INSTALL_DIR/bin</destination>
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56 </action>
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57 <action type="move_file">
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58 <source>bowtie-build</source>
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59 <destination>$INSTALL_DIR/bin</destination>
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60 </action>
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61 <action type="move_file">
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62 <source>bowtie-inspect</source>
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63 <destination>$INSTALL_DIR/bin</destination>
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64 </action>
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65 <action type="set_environment">
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66 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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67 </action>
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68 </actions>
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69 </install>
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70 <readme>
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71 Compiling Bowtie requires libpthread to be present on your system.
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72 </readme>
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73 </package>
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74
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75 <package name="gmap" version="2012-07-20">
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76 <install version="1.0">
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77 <actions>
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78 <action type="download_by_url" target_filename="gmap-2012-07-20.tar.gz">http://research-pub.gene.com/gmap/src/gmap-gsnap-2012-07-20.v2.tar.gz</action>
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79 <action type="shell_command">./configure</action>
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80 <action type="shell_command">make</action>
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81 <action type="move_file">
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82 <source>src/gmap</source>
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83 <destination>$INSTALL_DIR/bin</destination>
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84 </action>
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85 <action type="move_file">
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86 <source>src/gmapindex</source>
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87 <destination>$INSTALL_DIR/bin</destination>
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88 </action>
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89 <action type="move_file">
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90 <source>src/gsnap</source>
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91 <destination>$INSTALL_DIR/bin</destination>
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92 </action>
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93 <action type="move_file">
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94 <source>src/uniqscan</source>
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95 <destination>$INSTALL_DIR/bin</destination>
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96 </action>
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97 <action type="move_file">
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98 <source>src/iit_store</source>
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99 <destination>$INSTALL_DIR/bin</destination>
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100 </action>
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101 <action type="move_file">
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102 <source>src/iit_get</source>
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103 <destination>$INSTALL_DIR/bin</destination>
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104 </action>
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105 <action type="move_file">
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106 <source>src/atoiindex</source>
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107 <destination>$INSTALL_DIR/bin</destination>
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108 </action>
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109 <action type="move_file">
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110 <source>src/snpindex</source>
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111 <destination>$INSTALL_DIR/bin</destination>
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112 </action>
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113 <action type="move_file">
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114 <source>src/cmetindex</source>
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115 <destination>$INSTALL_DIR/bin</destination>
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116 </action>
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117 <action type="move_file">
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118 <source>src/get-genome</source>
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119 <destination>$INSTALL_DIR/bin</destination>
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120 </action>
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121 <action type="move_directory_files">
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122 <source_directory>util</source_directory>
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123 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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124 </action>
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125 <action type="set_environment">
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126 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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127 </action>
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128 </actions>
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129 </install>
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130 <readme>
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131 </readme>
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132 </package>
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133
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134 <package name="blat" version="34x10">
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135 <install version="1.0">
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136 <actions>
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137 <action type="download_by_url">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat</action>
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138 <action type="shell_command">chmod 755 blat</action>
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139 <action type="move_file">
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140 <source>blat</source>
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141 <destination>$INSTALL_DIR/bin</destination>
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142 </action>
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143 <action type="set_environment">
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144 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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145 </action>
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146 </actions>
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147 </install>
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148 <readme>
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149 This only handles blat for a non-commercial linux system.
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150
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151 Please note that the Blat source and executables are freely available for
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152 academic, nonprofit and personal use. Commercial licensing information is
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153 available on the Kent Informatics website (http://www.kentinformatics.com/).
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154 </readme>
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155 </package>
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156
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157 <package name="fatotwobit" version="34x10">
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158 <install version="1.0">
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159 <actions>
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160 <action type="download_by_url">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit</action>
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161 <action type="shell_command">chmod 755 faToTwoBit</action>
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162 <action type="move_file">
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163 <source>faToTwoBit</source>
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164 <destination>$INSTALL_DIR/bin</destination>
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165 </action>
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166 <action type="set_environment">
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167 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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168 </action>
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169 </actions>
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170 </install>
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171 <readme>
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172 This only handles faToTwoBit for a non-commercial linux system.
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173
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174 Please note that the source and executables are freely available for
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175 academic, nonprofit and personal use. Commercial licensing information is
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176 available on the Kent Informatics website (http://www.kentinformatics.com/).
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177 </readme>
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178 </package>
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179
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180 </tool_dependency>