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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="numpy" version="1.9">
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4 <repository changeset_revision="1e2b7e63dec2" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="samtools" version="0.1.19">
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7 <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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8 </package>
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9 <package name="lumpy" version="0.2.9">
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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/arq5x/lumpy-sv/archive/0.2.9.tar.gz</action>
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13 <action type="shell_command">make</action>
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14 <action type="move_directory_files">
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15 <source_directory>./bin</source_directory>
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16 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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17 </action>
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18 <action type="move_directory_files">
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19 <source_directory>./scripts</source_directory>
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20 <destination_directory>$INSTALL_DIR/scripts</destination_directory>
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21 </action>
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22 <action type="set_environment">
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23 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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24 <environment_variable action="set_to" name="LUMPY_SCRIPTS">$INSTALL_DIR/scripts</environment_variable>
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25 </action>
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26 </actions>
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27 </install>
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28 </package>
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29 </tool_dependency>
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