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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="bwa" version="0.7.12">
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4 <repository changeset_revision="67aa12c8d449" name="package_bwa_0_7_12" 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="1.2">
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7 <repository changeset_revision="5b7172f9b230" name="package_samtools_1_2" 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="python" version="2.7.10">
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10 <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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11 </package>
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12 <package name="bwameth" version="0.20">
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13 <install version="1.0">
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14 <actions>
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15 <action type="setup_python_environment">
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16 <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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17 <package name="python" version="2.7.10" />
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18 </repository>
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19 </action>
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20 <action type="set_environment">
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21 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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22 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
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23 </action>
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24 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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2
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25 <action type="shell_command">git clone https://github.com/brentp/bwa-meth && cd bwa-meth && git reset --hard 7dfec747105b9fa2cf1678bf5f67e860a0155d0e && python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action>
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26 </actions>
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27 </install>
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28 <readme>
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29 Installation of bwa-meth from Brent Pedersen
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30 https://github.com/brentp/bwa-meth
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31 </readme>
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32 </package>
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33 </tool_dependency>
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