<commit_before><tool_dependency>
    <package name="perl" version="5.18.1">
        <repository name="package_perl_5_18" owner="iuc" prior_installation_required="True" />
    </package>
    <package name="jbrowse" version="1.11.6">
        <install version="1.0">
            <actions>
                <action type="download_by_url" sha256sum="4beb1bf53d1843a96e326b71f814c0d55081a63b7204bf75e9c28b8b0e93cf4b">https://depot.galaxyproject.org/software/4beb1bf53d1843a96e326b71f814c0d55081a63b7204bf75e9c28b8b0e93cf4b</action>
                <action type="download_by_url" sha256sum="4beb1bf53d1843a96e326b71f814c0d55081a63b7204bf75e9c28b8b0e93cf4b">https://depot.galaxyproject.org/software/4beb1bf53d1843a96e326b71f814c0d55081a63b7204bf75e9c28b8b0e93cf4b</action>
                <action type="move_directory_files">
                    <source_directory>.</source_directory>
                    <destination_directory>$INSTALL_DIR</destination_directory>
                </action>
                <action type="setup_perl_environment">
                    <repository name="package_perl_5_18" owner="iuc">
                        <package name="perl" version="5.18.1" />
                    </repository>

                    <package sha256sum="3507f72541f66a2dce850b9b56771e5fccda3d215c52f74946c6e370c0f4a4da">https://depot.galaxyproject.org/software/3507f72541f66a2dce850b9b56771e5fccda3d215c52f74946c6e370c0f4a4da</package>
                    <package sha256sum="055c9ed6b6f85d3764834a90a933f13dc8cf417c349197da4eebc7bb824f821a">https://depot.galaxyproject.org/software/055c9ed6b6f85d3764834a90a933f13dc8cf417c349197da4eebc7bb824f821a</package>
                    <package sha256sum="55a414ce89eb7a5e9e84186f286b002054f10ae8ef4f8f2d61bb710e7549f16b">https://depot.galaxyproject.org/software/55a414ce89eb7a5e9e84186f286b002054f10ae8ef4f8f2d61bb710e7549f16b</package>
                    <package sha256sum="4ddbb3cb985a79f69a34e7c26cde1c81120d03487e87366f9a119f90f7bdfe88">https://depot.galaxyproject.org/software/4ddbb3cb985a79f69a34e7c26cde1c81120d03487e87366f9a119f90f7bdfe88</package>

                    <package sha256sum="219b8a97164efc2b46985e9178234683d675c2eec2b90fa925844680144c12a1">https://depot.galaxyproject.org/software/219b8a97164efc2b46985e9178234683d675c2eec2b90fa925844680144c12a1</package>

                    <package sha256sum="9fb0534bb7ef6ca1f6cc1dc3f29750d6d424394d14c40efdc77832fad3cebde8">https://depot.galaxyproject.org/software/9fb0534bb7ef6ca1f6cc1dc3f29750d6d424394d14c40efdc77832fad3cebde8</package>
                    <package sha256sum="47f9f03330b7595c94e73bdd17dc6682ba59d1cc89e63f4e319617f4bb122a64">https://depot.galaxyproject.org/software/47f9f03330b7595c94e73bdd17dc6682ba59d1cc89e63f4e319617f4bb122a64</package>

                    <package sha256sum="96de61bad187919bf632cfa657f1b9957ad47defcc90dad8ee1f50c955eedb86">https://depot.galaxyproject.org/software/96de61bad187919bf632cfa657f1b9957ad47defcc90dad8ee1f50c955eedb86</package>
                    <package sha256sum="ca3a089cb263ab6b9751df777cf6d3df3ba470d471d300a8076e4be6e288d057">https://depot.galaxyproject.org/software/ca3a089cb263ab6b9751df777cf6d3df3ba470d471d300a8076e4be6e288d057</package>
<commit_msg>Rebase against master with some manual corrections<commit_after><tool_dependency>
    <package name="perl" version="5.18.1">
        <repository name="package_perl_5_18" owner="iuc" prior_installation_required="True" />
    </package>
    <package name="jbrowse" version="1.11.6">
        <install version="1.0">
            <actions>
                <action type="download_by_url" sha256sum="4beb1bf53d1843a96e326b71f814c0d55081a63b7204bf75e9c28b8b0e93cf4b">https://depot.galaxyproject.org/software/4beb1bf53d1843a96e326b71f814c0d55081a63b7204bf75e9c28b8b0e93cf4b</action>
                <action type="move_directory_files">
                    <source_directory>.</source_directory>
                    <destination_directory>$INSTALL_DIR</destination_directory>
                </action>
                <action type="setup_perl_environment">
                    <repository name="package_perl_5_18" owner="iuc">
                        <package name="perl" version="5.18.1" />
                    </repository>

                    <package sha256sum="3507f72541f66a2dce850b9b56771e5fccda3d215c52f74946c6e370c0f4a4da">https://depot.galaxyproject.org/software/3507f72541f66a2dce850b9b56771e5fccda3d215c52f74946c6e370c0f4a4da</package>
                    <package sha256sum="055c9ed6b6f85d3764834a90a933f13dc8cf417c349197da4eebc7bb824f821a">https://depot.galaxyproject.org/software/055c9ed6b6f85d3764834a90a933f13dc8cf417c349197da4eebc7bb824f821a</package>
                    <package sha256sum="55a414ce89eb7a5e9e84186f286b002054f10ae8ef4f8f2d61bb710e7549f16b">https://depot.galaxyproject.org/software/55a414ce89eb7a5e9e84186f286b002054f10ae8ef4f8f2d61bb710e7549f16b</package>
                    <package sha256sum="4ddbb3cb985a79f69a34e7c26cde1c81120d03487e87366f9a119f90f7bdfe88">https://depot.galaxyproject.org/software/4ddbb3cb985a79f69a34e7c26cde1c81120d03487e87366f9a119f90f7bdfe88</package>

                    <package sha256sum="219b8a97164efc2b46985e9178234683d675c2eec2b90fa925844680144c12a1">https://depot.galaxyproject.org/software/219b8a97164efc2b46985e9178234683d675c2eec2b90fa925844680144c12a1</package>

                    <package sha256sum="9fb0534bb7ef6ca1f6cc1dc3f29750d6d424394d14c40efdc77832fad3cebde8">https://depot.galaxyproject.org/software/9fb0534bb7ef6ca1f6cc1dc3f29750d6d424394d14c40efdc77832fad3cebde8</package>
                    <package sha256sum="47f9f03330b7595c94e73bdd17dc6682ba59d1cc89e63f4e319617f4bb122a64">https://depot.galaxyproject.org/software/47f9f03330b7595c94e73bdd17dc6682ba59d1cc89e63f4e319617f4bb122a64</package>

                    <package sha256sum="96de61bad187919bf632cfa657f1b9957ad47defcc90dad8ee1f50c955eedb86">https://depot.galaxyproject.org/software/96de61bad187919bf632cfa657f1b9957ad47defcc90dad8ee1f50c955eedb86</package>
                    <package sha256sum="ca3a089cb263ab6b9751df777cf6d3df3ba470d471d300a8076e4be6e288d057">https://depot.galaxyproject.org/software/ca3a089cb263ab6b9751df777cf6d3df3ba470d471d300a8076e4be6e288d057</package>

{'fraction_non_alphanumeric': 0.08239820455274126, 'fraction_numerical': 0.28326386662391795, 'mean_word_length': 4.718606782768103, 'pattern_counts': {'":': 0, '<': 79, '<?xml version=': 0, '>': 79, 'https://': 21, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 3, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6609529', 'n_tokens_mistral': 3499, 'n_tokens_neox': 2570, 'n_words': 109}