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4
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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6
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3 <package name="samtools" version="0.1.19">
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4 <repository changeset_revision="54195f1d4b0f" name="package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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7
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6 <package name="R_3_0_1" version="3.0.1">
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7 <repository changeset_revision="e16e08f41ed7" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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8 </package>
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6
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9 <package name="blockclust" version="1.0">
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4
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10 <install version="1.0">
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11 <actions>
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12 <action type="download_by_url">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-1.0.tar.gz</action>
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13 <action type="shell_command">make</action>
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14 <action type="move_file">
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15 <source>BlockClust</source>
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16 <destination>$INSTALL_DIR/bin</destination>
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17 </action>
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18 <action type="move_file">
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19 <source>BlockClustPipeLine.pl</source>
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20 <destination>$INSTALL_DIR/bin</destination>
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21 </action>
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22 <action type="move_file">
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5
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23 <source>perf</source>
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24 <destination>$INSTALL_DIR/bin</destination>
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25 </action>
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26 <action type="move_file">
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4
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27 <source>blockclust.config</source>
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28 <destination>$INSTALL_DIR/data/</destination>
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29 </action>
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6
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30 <action type="move_file">
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31 <source>rfam_map.txt</source>
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32 <destination>$INSTALL_DIR/data/</destination>
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33 </action>
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4
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34 <action type="make_directory">$INSTALL_DIR/data/annotations</action>
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35 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/dm3.tar.gz</action>
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36 <action type="shell_command">tar xfvz dm3.tar.gz -C $INSTALL_DIR/data/annotations/</action>
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37 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/hg19.tar.gz</action>
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38 <action type="shell_command">tar xfvz hg19.tar.gz -C $INSTALL_DIR/data/annotations/</action>
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39 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/mm10.tar.gz</action>
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40 <action type="shell_command">tar xfvz mm10.tar.gz -C $INSTALL_DIR/data/annotations/</action>
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41 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/panTro4.tar.gz</action>
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42 <action type="shell_command">tar xfvz panTro4.tar.gz -C $INSTALL_DIR/data/annotations/</action>
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43 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/rheMac3.tar.gz</action>
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44 <action type="shell_command">tar xfvz rheMac3.tar.gz -C $INSTALL_DIR/data/annotations/</action>
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45 <action type="set_environment">
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6
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46 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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47 <environment_variable action="prepend_to" name="BLOCKCLUST_DATA_PATH">$INSTALL_DIR/data</environment_variable>
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4
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48 </action>
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5
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49 <action type="setup_r_environment">
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50 <repository changeset_revision="e16e08f41ed7" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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51 <package name="R_3_0_1" version="3.0.1" />
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52 </repository>
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53 <r_package>http://cran.r-project.org/src/contrib/ggplot2_0.9.3.1.tar.gz</r_package>
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54 <r_package>http://cran.r-project.org/src/contrib/ape_3.0-11.tar.gz</r_package>
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55 </action>
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56 <action type="set_environment">
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57 <environment_variable action="append_to" name="R_LIBS">$INSTALL_DIR</environment_variable>
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58 </action>
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4
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59 </actions>
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60 </install>
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61 <readme>
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62
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63 </readme>
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64 </package>
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65 </tool_dependency>
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