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39
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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="boost" version="1.53.0">
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5 <repository changeset_revision="cee17eb9de41" name="package_boost_1_53" owner="iuc" 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="bamtools" version="2.3.0">
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9 <repository changeset_revision="ad46b5210186" name="package_bamtools_2_3_0" owner="malbuquerque" 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="seqtk" version="1.0.0">
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13 <repository changeset_revision="35f0f4568ded" name="package_seqtk_1_0_0" owner="malbuquerque" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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14 </package>
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15
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16 <package name="delly" version="0.6.1">
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17 <install version="1.0">
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18 <actions>
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19 <action type="set_environment_for_install">
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20 <repository changeset_revision="cee17eb9de41" name="package_boost_1_53" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
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21 <package name="boost" version="1.53.0" />
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22 </repository>
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23 </action>
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24
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25 <action type="set_environment_for_install">
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26 <repository changeset_revision="ad46b5210186" name="package_bamtools_2_3_0" owner="malbuquerque" toolshed="https://toolshed.g2.bx.psu.edu">
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27 <package name="bamtools" version="2.3.0" />
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28 </repository>
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29 </action>
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30
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31 <action type="set_environment_for_install">
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32 <repository changeset_revision="35f0f4568ded" name="package_seqtk_1_0_0" owner="malbuquerque" toolshed="https://toolshed.g2.bx.psu.edu">
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33 <package name="seqtk" version="1.0.0" />
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34 </repository>
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35 </action>
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36
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37 <action type="download_by_url">https://github.com/tobiasrausch/delly/archive/v0.6.1.tar.gz</action>
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38 <action type="shell_command">pwd > ~/delly.pwd.txt</action>
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39 <action type="shell_command">echo $INSTALL_DIR > ~/delly.dir.txt</action>
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40 <action type="shell_command">sleep 25</action>
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41 <action type="shell_command">make -f $REPOSITORY_INSTALL_DIR/Makefile all BOOST_ROOT=$BOOST_ROOT_DIR/ BAMTOOLS_ROOT=$BAMTOOLS_ROOT/ SEQTK_ROOT=$SEQTK_ROOT/</action>
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42 <action type="move_directory_files">
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43 <source_directory>.</source_directory>
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44 <destination_directory>$INSTALL_DIR</destination_directory>
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45 </action>
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46 <action type="set_environment">
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47 <environment_variable action="set_to" name="DELLY_DIR">$INSTALL_DIR</environment_variable>
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48 </action>
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49 </actions>
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50 </install>
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51 </package>
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52
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53 </tool_dependency>
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