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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <set_environment version="1.0">
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4 <environment_variable name="JAR_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
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5 </set_environment>
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6
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7 <set_environment version="1.0">
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8 <environment_variable name="CIRCOS_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
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9 </set_environment>
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10
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11 <package name="circos" version="0.64">
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12 <install version="1.0">
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13 <actions>
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14 <!-- Downloads the Circos software from its website and unpacks it -->
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15 <action type="download_by_url">http://circos.ca/distribution/circos-0.64.tgz </action>
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16 <action type="move_directory_files">
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17 <source_directory>.</source_directory>
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18 <destination_directory>$INSTALL_DIR/</destination_directory>
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19 </action>
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20 <action type="set_environment">
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21 <environment_variable name="CIRCOS_PATH" action="set_to">$INSTALL_DIR</environment_variable>
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22 </action>
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23 </actions>
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24 </install>
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25 <readme>
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26 Downloads and installs Circos (v.0.64) for use in visualization. Requires perl to be installed.
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27 </readme>
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10
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28 </package>
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29
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30 <package name="R_3_0_1" version="3.0.1">
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31 <install version="1.0">
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32 <actions>
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33 <action type="download_by_url">http://cran.ms.unimelb.edu.au/src/base/R-3/R-3.0.1.tar.gz</action>
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34 <!--<action type="set_environment_for_install">
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35 <repository name="package_readline_6_2" owner="iuc">
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36 <package name="readline" version="6.2" />
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37 </repository>
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38 </action>-->
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39
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40 <action type="shell_command">
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41 ./configure --with-readline=no --enable-R-shlib --with-x=no --libdir=$INSTALL_DIR/lib/ --bindir=$INSTALL_DIR/bin/ --datarootdir=$INSTALL_DIR/share/
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42 </action>
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43 <action type="shell_command">make</action>
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44 <action type="shell_command">make install</action>
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45 <action type="set_environment">
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46 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
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47 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
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48 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
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49 <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/R/lib</environment_variable>
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50 <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
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51 <environment_variable action="set_to" name="R_PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
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52 </action>
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53 </actions>
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54 </install>
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55 <readme>R is a free software environment for statistical computing and graphics. http://www.r-project.org/</readme>
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56 </package>
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2
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57
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58 </tool_dependency>
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