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2
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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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12
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30 <set_environment version="1.0">
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31 <environment_variable name="R_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
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32 </set_environment>
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14
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33
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12
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34 <package name="R_3_0_2" version="3.0.2">
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10
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35 <install version="1.0">
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36 <actions>
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12
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37 <action type="download_by_url">http://cran.ms.unimelb.edu.au/src/base/R-3/R-3.0.2.tar.gz</action>
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38 <action type="set_environment_for_install">
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39 <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
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40 <package name="readline" version="6.2" />
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41 </repository>
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12
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42 <repository changeset_revision="9ed7af129bd3" name="package_ncurses_5_9" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
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43 <package name="ncurses" version="5.9" />
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44 </repository>
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45 <repository changeset_revision="51f77dcf27bd" name="package_libpng_1_6_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu">
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46 <package name="libpng" version="1.6.7" />
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47 </repository>
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48 </action>
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49
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50 <action type="shell_command">
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51 ./configure CPPFLAGS="-I$READLINE_INCLUDE_PATH -I${LIBPNG_ROOT}/include" LDFLAGS="-L$READLINE_LIB_PATH -L$NCURSES_LIB_PATH -L${LIBPNG_ROOT}/lib -lreadline -lncurses" --with-libpng --enable-R-shlib --with-x=no --libdir=$INSTALL_DIR/lib/ --bindir=$INSTALL_DIR --datarootdir=$INSTALL_DIR/share/
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52 </action>
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53
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54 <action type="shell_command">make</action>
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55 <action type="shell_command">make install</action>
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56 <action type="set_environment">
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57 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
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58 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
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59 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
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60 <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/R/lib</environment_variable>
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61 <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
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62 <environment_variable action="set_to" name="R_PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
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63 </action>
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64 </actions>
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65 </install>
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66 <readme>R is a free software environment for statistical computing and graphics. http://www.r-project.org/</readme>
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12
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67 </package>
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2
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68
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69 </tool_dependency>
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