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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3
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4 <package name="cmake" version="3.1.0">
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8
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5 <repository changeset_revision="782e014e71f9" name="package_cmake_3_1_0" owner="malbuquerque" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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6 </package>
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7
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8 <package name="samtools" version="0.1.18">
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5
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9 <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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10 </package>
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11
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12 <package name="bamtools" version="2.3.0">
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13 <install version="1.0">
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14 <actions>
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9
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15
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16 <action type="shell_command">pwd > ~/whereami-2</action>
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17
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6
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18 <action type="set_environment_for_install">
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8
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19 <repository changeset_revision="782e014e71f9" name="package_cmake_3_1_0" owner="malbuquerque" toolshed="https://toolshed.g2.bx.psu.edu">
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6
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20 <package name="cmake" version="3.1.0" />
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21 </repository>
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22 </action>
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23
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9
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24 <action type="shell_command">pwd > ~/whereami-1</action>
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25
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6
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26 <action type="set_environment_for_install">
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27 <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu">
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7
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28 <package name="samtools" version="0.1.18" />
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6
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29 </repository>
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30 </action>
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9
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31
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32 <action type="shell_command">pwd > ~/whereami0</action>
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33 <action type="download_by_url">https://github.com/pezmaster31/bamtools/archive/v2.3.0.tar.gz</action>
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8
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34 <action type="shell_command">pwd > ~/whereami</action>
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35 <action type="shell_command">mkdir build</action>
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8
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36 <action type="shell_command">pwd > ~/whereami2</action>
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3
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37 <action type="change_directory">build</action>
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8
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38 <action type="shell_command">pwd > ~/whereami3</action>
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3
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39 <action type="shell_command">cmake ..</action>
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8
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40 <action type="shell_command">pwd > ~/whereami4</action>
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41 <action type="shell_command">make</action>
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8
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42 <action type="shell_command">pwd > ~/whereami5</action>
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4
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43 <action type="change_directory">..</action>
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8
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44 <action type="shell_command">pwd > ~/whereami6</action>
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0
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45
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46 <action type="move_directory_files">
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47 <source_directory>./</source_directory>
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48 <destination_directory>$INSTALL_DIR</destination_directory>
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49 </action>
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50
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51 <action type="set_environment">
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52 <environment_variable action="set_to" name="BAMTOOLS_ROOT">$INSTALL_DIR</environment_variable>
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53 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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54 </action>
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55
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56 </actions>
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57 </install>
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58 </package>
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59
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60 </tool_dependency>
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