<commit_before><?xml version="1.0"?>
<tool_dependency>
    <package name="mothur" version="1.36.1">
        <install version="1.0">
            <actions>
                <action type="download_by_url" sha256sum="dfdc486b24d14d776d45df9d523e62a49332ff0e3def4e0bb95cfbe369638f22">https://github.com/mothur/mothur/archive/v1.36.1.zip</action>
                <action type="set_environment_for_install">
                    <repository name="package_legacy_blast_2_2_22" owner="iuc">
                        <package name="legacy_blast" version="2.2.22" />
                    </repository>
                    <repository name="package_boost_1_57" owner="iuc">
                        <package name="boost" version="1.57" />
                    </repository>
                    <repository name="package_zlib_1_2_8" owner="iuc">
                        <package name="zlib" version="1.2.8" />
                    </repository>
                </action>
                <action type="shell_command">chmod u+x source/uchime_src/mk</action>
                <action type="shell_command">
                    test $(uname) = Linux &amp;&amp;
                    perl -i.bak -pe 's/(USEREADLINE.+) = yes/$1 = no/; s/TARGET_ARCH \+= -arch x86_64//; s/#(CXXFLAGS.+-mtune=native -march=native -m64)/$1/;' source/makefile ||
                    true
                </action>
                <action type="shell_command">sed -i 's/\ \ \ \ /\t/g' source/makefile;</action>
                <action type="shell_command">sed -i '141d;151d;152d' source/makefile;</action>
                <action type="shell_command">sed -i 's/fortranSource//g' source/makefile;</action>
                <action type="shell_command">sed -i 's/\/usr\/local/${BOOST_ROOT_DIR}\/boost/g' source/makefile;</action>
                <action type="shell_command">sed -i 's/\${BOOST_LIBRARY_DIR}zlib.a/${ZLIB_ROOT_DIR}\/lib\/libz.a/' source/makefile</action>

                <action type="shell_command">cd source; make -j 2;</action>
                <action type="move_file"><commit_msg>Use OS X-compatible sed syntax<commit_after><?xml version="1.0"?>
<tool_dependency>
    <package name="mothur" version="1.36.1">
        <install version="1.0">
            <actions>
                <action type="download_by_url" sha256sum="dfdc486b24d14d776d45df9d523e62a49332ff0e3def4e0bb95cfbe369638f22">https://github.com/mothur/mothur/archive/v1.36.1.zip</action>
                <action type="set_environment_for_install">
                    <repository name="package_legacy_blast_2_2_22" owner="iuc">
                        <package name="legacy_blast" version="2.2.22" />
                    </repository>
                    <repository name="package_boost_1_57" owner="iuc">
                        <package name="boost" version="1.57" />
                    </repository>
                    <repository name="package_zlib_1_2_8" owner="iuc">
                        <package name="zlib" version="1.2.8" />
                    </repository>
                </action>
                <action type="shell_command">chmod u+x source/uchime_src/mk</action>
                <action type="shell_command">
                    test $(uname) = Linux &amp;&amp;
                    perl -i.bak -pe 's/(USEREADLINE.+) = yes/$1 = no/; s/TARGET_ARCH \+= -arch x86_64//; s/#(CXXFLAGS.+-mtune=native -march=native -m64)/$1/;' source/makefile ||
                    true
                </action>
                <action type="shell_command">sed -i.bak -e 's/\ \ \ \ /\t/g' source/makefile;</action>
                <action type="shell_command">sed -i.bak -e '141d;151d;152d' source/makefile;</action>
                <action type="shell_command">sed -i.bak -e 's/fortranSource//g' source/makefile;</action>
                <action type="shell_command">sed -i.bak -e 's/\/usr\/local/${BOOST_ROOT_DIR}\/boost/g' source/makefile;</action>
                <action type="shell_command">sed -i.bak -e 's/\${BOOST_LIBRARY_DIR}zlib.a/${ZLIB_ROOT_DIR}\/lib\/libz.a/' source/makefile</action>

                <action type="shell_command">cd source; make -j 2;</action>
                <action type="move_file">
{'fraction_non_alphanumeric': 0.15516409266409267, 'fraction_numerical': 0.04343629343629344, 'mean_word_length': 1.9670722977809592, 'pattern_counts': {'":': 0, '<': 73, '<?xml version=': 2, '>': 73, 'https://': 2, 'lorem ipsum': 0, 'www.': 0, 'xml': 2}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '671667', 'n_tokens_mistral': 1431, 'n_tokens_neox': 1290, 'n_words': 198}