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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool_dependency>
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3 <!-- This package will not track any version of the underlying toools.
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4 Any hint how to compile or ship the binaries without violating the license is very much appreciated.
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5 -->
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6 <package name="ucsc_tools" version="0.1">
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7 <install version="1.0">
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8 <actions>
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9 <action type="download_binary">
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10 <url_template os="linux" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
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11 <url_template os="darwin" architecture="i686">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
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12 <url_template os="darwin" architecture="i386">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
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13 <url_template os="darwin" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig</url_template>
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14 </action>
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15 <action type="chmod">
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16 <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
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17 </action>
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18 <action type="download_binary">
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19 <url_template os="linux" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template>
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20 <url_template os="darwin" architecture="i686">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
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21 <url_template os="darwin" architecture="i386">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
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22 <url_template os="darwin" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo</url_template>
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23 </action>
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24 <action type="chmod">
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25 <file mode="755">$INSTALL_DIR/bigWigInfo</file>
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26 </action>
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27 <action type="download_binary">
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28 <url_template os="linux" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigToBedGraph</url_template>
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29 <url_template os="darwin" architecture="i686">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph</url_template>
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30 <url_template os="darwin" architecture="i386">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph</url_template>
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31 <url_template os="darwin" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigToBedGraph</url_template>
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32 </action>
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33 <action type="chmod">
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34 <file mode="755">$INSTALL_DIR/bigWigToBedGraph</file>
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35 </action>
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36 <action type="set_environment">
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37 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
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38 <environment_variable name="UCSC_TOOLS_ROOT_PATH" action="set_to">$INSTALL_DIR</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>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme>
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43 </package>
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44 </tool_dependency>
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