<commit_before><?xml version='1.0' encoding='utf-8'?>
<tool_dependency>
    <package name="numpy" version="1.9">
        <repository name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" />
    </package>
    <package name="pybigwig" version="0.2.8">
        <repository name="package_python_2_7_10_pybigwig_0_2_8" owner="iuc" prior_installation_required="True"/>
    </package>
    <package name="matplotlib" version="1.4">
        <repository name="package_python_2_7_matplotlib_1_4" owner="iuc" prior_installation_required="True" />
    </package>
    <package name="scipy" version="0.14">
        <repository name="package_python_2_7_scipy_0_14" owner="iuc" prior_installation_required="True" />
    </package>
    <package name="pysam" version="0.8.3">
        <repository name="package_python_2_7_pysam_0_8_3" owner="iuc" prior_installation_required="True" />
    </package>
    <package name="python" version="2.7.10">
        <repository name="package_python_2_7_10" owner="iuc" prior_installation_required="True" />
    </package>
    <package name="deepTools" version="2.3.3">
        <install version="1.0">
            <actions>
                <action type="setup_python_environment">
                    <repository name="package_python_2_7_10" owner="iuc">
                        <package name="python" version="2.7.10" />
                    </repository>
                    <repository name="package_python_2_7_pysam_0_8_3" owner="iuc">
                        <package name="pysam" version="0.8.3" />
                    </repository>
                    <repository name="package_python_2_7_numpy_1_9" owner="iuc">
                        <package name="numpy" version="1.9" />
                    </repository>
                    <repository name="package_python_2_7_matplotlib_1_4" owner="iuc">
                        <package name="matplotlib" version="1.4" />
                    </repository>
                    <repository name="package_python_2_7_scipy_0_14" owner="iuc">
                        <package name="scipy" version="0.14" />
                    </repository>
                    <repository name="package_python_2_7_10_pybigwig_0_2_8" owner="iuc">
                        <package name="pybigwig" version="0.2.8" />
                    </repository>
                    <package sha256sum="047511c9a6231207fa6ee49f901f9afa0f81c57e4bc03840392e48ed67d97203">https://pypi.python.org/packages/c1/03/982c3656e85e6f264b37d5f6e594d030d6dd99064913eb423d2b40fcebe3/deepTools-2.3.3.tar.gz</package>
                </action>

                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR</environment_variable>
                    <environment_variable name="DEEPTOOLS_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable>
                    <environment_variable name="DEEPTOOLS_PYTHONPATH" action="set_to">$INSTALL_DIR</environment_variable>
                    <environment_variable name="DEEPTOOLS_PATH" action="set_to">$INSTALL_DIR/bin</environment_variable>
                    <!-- libpng lib path -->
                    <environment_variable action="set_to" name="LIBPNG_LIB_PATH">$ENV[LIBPNG_LIB_PATH]</environment_variable>
                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LIBPNG_LIB_PATH]</environment_variable>
                    <!-- disable the config file of deepTools -->
                    <environment_variable name="DEEP_TOOLS_NO_CONFIG" action="set_to">TRUE</environment_variable>
                </action>
             </actions>
         </install>
         <readme>
            Installation of deepTools from <NAME>.
            https://github.com/fidelram/deepTools
         </readme>
     </package>
</tool_dependency><commit_msg>The twobitreader dependency was missing<commit_after><?xml version='1.0' encoding='utf-8'?>
<tool_dependency>
    <package name="numpy" version="1.9">
        <repository name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" />
    </package>
    <package name="pybigwig" version="0.2.8">
        <repository name="package_python_2_7_10_pybigwig_0_2_8" owner="iuc" prior_installation_required="True"/>
    </package>
    <package name="twobitreader" version="3.1.4">
        <repository name="package_python_2_7_10_twobitreader_3_1_4" owner="iuc" prior_installation_required="True"/>
    </package>
    <package name="matplotlib" version="1.4">
        <repository name="package_python_2_7_matplotlib_1_4" owner="iuc" prior_installation_required="True" />
    </package>
    <package name="scipy" version="0.14">
        <repository name="package_python_2_7_scipy_0_14" owner="iuc" prior_installation_required="True" />
    </package>
    <package name="pysam" version="0.8.3">
        <repository name="package_python_2_7_pysam_0_8_3" owner="iuc" prior_installation_required="True" />
    </package>
    <package name="python" version="2.7.10">
        <repository name="package_python_2_7_10" owner="iuc" prior_installation_required="True" />
    </package>
    <package name="deepTools" version="2.3.3">
        <install version="1.0">
            <actions>
                <action type="setup_python_environment">
                    <repository name="package_python_2_7_10" owner="iuc">
                        <package name="python" version="2.7.10" />
                    </repository>
                    <repository name="package_python_2_7_pysam_0_8_3" owner="iuc">
                        <package name="pysam" version="0.8.3" />
                    </repository>
                    <repository name="package_python_2_7_numpy_1_9" owner="iuc">
                        <package name="numpy" version="1.9" />
                    </repository>
                    <repository name="package_python_2_7_matplotlib_1_4" owner="iuc">
                        <package name="matplotlib" version="1.4" />
                    </repository>
                    <repository name="package_python_2_7_scipy_0_14" owner="iuc">
                        <package name="scipy" version="0.14" />
                    </repository>
                    <repository name="package_python_2_7_10_pybigwig_0_2_8" owner="iuc">
                        <package name="pybigwig" version="0.2.8" />
                    </repository>
                    <repository name="package_python_2_7_10_twobitreader_3_1_4" owner="iuc">
                        <package name="twobitreader" version="3.1.4" />
                    </repository>
                    <package sha256sum="047511c9a6231207fa6ee49f901f9afa0f81c57e4bc03840392e48ed67d97203">https://pypi.python.org/packages/c1/03/982c3656e85e6f264b37d5f6e594d030d6dd99064913eb423d2b40fcebe3/deepTools-2.3.3.tar.gz</package>
                </action>

                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR</environment_variable>
                    <environment_variable name="DEEPTOOLS_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable>
                    <environment_variable name="DEEPTOOLS_PYTHONPATH" action="set_to">$INSTALL_DIR</environment_variable>
                    <environment_variable name="DEEPTOOLS_PATH" action="set_to">$INSTALL_DIR/bin</environment_variable>
                    <!-- libpng lib path -->
                    <environment_variable action="set_to" name="LIBPNG_LIB_PATH">$ENV[LIBPNG_LIB_PATH]</environment_variable>
                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LIBPNG_LIB_PATH]</environment_variable>
                    <!-- disable the config file of deepTools -->
                    <environment_variable name="DEEP_TOOLS_NO_CONFIG" action="set_to">TRUE</environment_variable>
                </action>
             </actions>
         </install>
         <readme>
            Installation of deepTools from <NAME>.
            https://github.com/fidelram/deepTools
         </readme>
     </package>
</tool_dependency>
{'fraction_non_alphanumeric': 0.1234849393975759, 'fraction_numerical': 0.0484819392775711, 'mean_word_length': 2.5539445628997868, 'pattern_counts': {'":': 0, '<': 153, '<?xml version=': 2, '>': 153, 'https://': 4, 'lorem ipsum': 0, 'www.': 0, 'xml': 2}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '7487408', 'n_tokens_mistral': 2714, 'n_tokens_neox': 2515, 'n_words': 324}