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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="grabix" version="0.1.3">
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4 <repository changeset_revision="ea8dd47bccea" name="package_grabix_0_1_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="tabix" version="0.2.6">
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7 <repository changeset_revision="c1743e071a28" name="package_tabix_0_2_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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8 </package>
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9 <package name="samtools" version="0.1.19">
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10 <repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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11 </package>
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12 <package name="bedtools" version="2.19.1">
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13 <repository changeset_revision="3ad963111153" name="package_bedtools_2_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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14 </package>
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15 <package name="pybedtools" version="0.6.6">
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16 <repository changeset_revision="cc2ed79fc537" name="package_pybedtools_0_6_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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17 </package>
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18 <package name="gemini" version="0.9.1">
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19 <install version="1.0">
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20 <actions>
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21 <!-- first action is always downloading -->
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22 <action type="download_by_url">https://github.com/arq5x/gemini/archive/v0.9.1.tar.gz</action>
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23
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24 <!-- populate the environment variables from the dependend repos -->
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25 <action type="set_environment_for_install">
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26 <repository changeset_revision="c1743e071a28" name="package_tabix_0_2_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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27 <package name="tabix" version="0.2.6" />
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28 </repository>
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29 <repository changeset_revision="ea8dd47bccea" name="package_grabix_0_1_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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30 <package name="grabix" version="0.1.3" />
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31 </repository>
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32 <repository changeset_revision="cc2ed79fc537" name="package_pybedtools_0_6_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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33 <package name="pybedtools" version="0.6.6" />
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34 </repository>
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35 </action>
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36
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37 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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38 <action type="shell_command">
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39 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&
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40 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
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41 </action>
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42
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43 <action type="set_environment">
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44 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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45 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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46 <environment_variable action="set_to" name="PYTHONPATH_GEMINI">$INSTALL_DIR/lib/python</environment_variable>
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47 <environment_variable action="set_to" name="PATH_GEMINI">$INSTALL_DIR/bin</environment_variable>
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48 <environment_variable action="set_to" name="GEMINI_ROOT_DIR">$INSTALL_DIR</environment_variable>
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49 </action>
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50 </actions>
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51 </install>
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52 <readme>Compiling GEMINI requires a recent c++ compiler, usually gcc.</readme>
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53 </package>
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54 </tool_dependency>
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