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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="tabix" version="0.2.6">
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2
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4 <repository changeset_revision="54f8b9bf9b6c" name="package_tabix_0_2_6" 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="samtools" version="0.1.19">
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3
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7 <repository changeset_revision="0e56e4dac6e7" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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8 </package>
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9 <package name="bedtools" version="2.19.1">
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10 <repository changeset_revision="3ad963111153" name="package_bedtools_2_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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11 </package>
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12 <package name="cython" version="0.20.1">
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13 <repository changeset_revision="749f11b9358a" name="package_cython_0_20_1" 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 <install version="1.0">
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17 <actions>
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18 <!-- first action is always downloading -->
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19 <action type="download_by_url">https://github.com/daler/pybedtools/archive/v0.6.6.tar.gz</action>
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20
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21 <!-- populate the environment variables from the dependend repos -->
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22 <action type="set_environment_for_install">
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23 <repository changeset_revision="749f11b9358a" name="package_cython_0_20_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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24 <package name="cython" version="0.20.1" />
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25 </repository>
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26 </action>
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27
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28 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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29 <action type="shell_command">
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30 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&
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31 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
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32 </action>
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33
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34 <action type="set_environment">
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35 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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36 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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37 <environment_variable action="set_to" name="PYTHONPATH_PYBEDTOOLS">$INSTALL_DIR/lib/python</environment_variable>
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38 <environment_variable action="set_to" name="PATH_PYBEDTOOLS">$INSTALL_DIR/bin</environment_variable>
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39 <environment_variable action="set_to" name="PYBEDTOOLS_ROOT_DIR">$INSTALL_DIR</environment_variable>
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40 </action>
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41 </actions>
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42 </install>
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43 <readme>Compiling pybedtools requires cython and the gcc compiler.
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44 https://github.com/daler/pybedtools
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45 </readme>
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46 </package>
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47 </tool_dependency>
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