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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>runbib</title><link rel="stylesheet" type="text/css" href="manual.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.79.1" /><link rel="home" href="index.html" title="RefDB handbook" /><link rel="up" href="ch15.html" title="Chapter 15. Tools for bibliographies" /><link rel="prev" href="re21.html" title="refdbnd" /><link rel="next" href="re23.html" title="runbib-missing" /></head><body><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">runbib</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="re21.html">Prev</a> </td><th width="60%" align="center">Chapter 15. Tools for bibliographies</th><td width="20%" align="right"> <a accesskey="n" href="re23.html">Next</a></td></tr></table><hr /></div><div class="refentry"><a id="refentry-runbib"></a><div class="titlepage"></div><div class="refnamediv"><a id="runbib-name"></a><h2>Name</h2><p>runbib — creates RefDB bibliographies</p></div><div class="refsynopsisdiv"><a id="runbib-synopsis"></a><h2>Synopsis</h2><div class="cmdsynopsis"><p><code class="command">runbib</code> [<code class="option">-a</code> <em class="replaceable"><code>fo-driver</code></em>] [<code class="option">-b</code> <em class="replaceable"><code>html-driver</code></em>] [<code class="option">-c</code> <em class="replaceable"><code>xhtml-driver</code></em>] [<code class="option">-d</code> <em class="replaceable"><code>database</code></em>] [<code class="option">-E</code> <em class="replaceable"><code>encoding</code></em>] [<code class="option">-G</code> <em class="replaceable"><code>css-file</code></em>] [<code class="option">-h</code> ] [<code class="option">-i</code> <em class="replaceable"><code>IP-address</code></em>] [<code class="option">-I</code> <em class="replaceable"><code>name</code></em>] [<code class="option">-j</code> <em class="replaceable"><code>jade-args</code></em>] [<code class="option">-N</code> <em class="replaceable"><code>number</code></em>] [<code class="option">-r</code> ] [<code class="option">-s</code> ] [<code class="option">-S</code> <em class="replaceable"><code>style</code></em>] [<code class="option">-t</code> <em class="replaceable"><code>output-type</code></em>] [<code class="option">-u</code> <em class="replaceable"><code>name</code></em>] [<code class="option">-w</code> <em class="replaceable"><code>password</code></em>] <em class="replaceable"><code>filename</code></em> </p></div></div><div class="refsect1"><a id="runbib-description"></a><h2>Description</h2><p>This shell script is a wrapper for the bibliography client <a class="link" href="re20.html" title="refdbib">refdbib</a>(1) to simplify the creation of bibliographies. For SGML and XML documents, runbib first runs openjade or xsltproc(1), respectively, to retrieve a list of citations from your source document. Then it runs refdbib(1) to generate the bibliography as an external entity based on the extracted citation information. It will also create stylesheet driver files with the formatting information for subsequent document transformations. For BibTeX documents, runbib uses the information in the .aux file to retrieve a bibliography file that you can use as an input file for bibtex(1).</p></div><div class="refsect1"><a id="runbib-options"></a><h2>Options</h2><div class="variablelist"><dl class="variablelist"><dt><span class="term"><code class="option">-a</code> <em class="replaceable"><code>fo-driver</code></em></span></dt><dd><p>The full path of a custom XSL driver file for printed output. This file has to import the appropriate RefDB fo driver file.</p></dd><dt><span class="term"><code class="option">-b</code> <em class="replaceable"><code>html-driver</code></em></span></dt><dd><p>The full path of a custom XSL driver file for HTML output. This file has to import the appropriate RefDB html driver file.</p></dd><dt><span class="term"><code class="option">-c</code> <em class="replaceable"><code>xhtml-driver</code></em></span></dt><dd><p>The full path of a custom XSL driver file for XHTML output. This file has to import the appropriate RefDB xhtml driver file.</p></dd><dt><span class="term"><code class="option">-d</code> <em class="replaceable"><code>database</code></em></span></dt><dd><p>The name of the default database.</p></dd><dt><span class="term"><code class="option">-E</code> <em class="replaceable"><code>encoding</code></em></span></dt><dd><p>Select an output character encoding. If this option is not used, the bibliography data will use the character encoding of the database. See iconv_open(3) for a list of available encodings.</p></dd><dt><span class="term"><code class="option">-G</code> <em class="replaceable"><code>CSS-file</code></em></span></dt><dd><p>Set the path or the URL of a CSS file to be used by the (x)html output</p></dd><dt><span class="term"><code class="option">-h</code></span></dt><dd><p>Displays help and usage screen, then exits.</p></dd><dt><span class="term"><code class="option">-i</code> <em class="replaceable"><code>IP-address</code></em></span></dt><dd><p>Set the IP address of the box which is running the application server refdbd(1). Instead of the IP address you can also specify the hostname as long as it can be properly resolved by your system.</p></dd><dt><span class="term"><code class="option">-I</code> <em class="replaceable"><code>name</code></em></span></dt><dd><p>Change the value of an entity declaration to include marked sections. Multiple entries are possible. These are passed as <code class="option">-i</code> options to Jade/OpenJade.</p></dd><dt><span class="term"><code class="option">-j</code> <em class="replaceable"><code>jade-args</code></em></span></dt><dd><p>Set additional command line options for Jade/OpenJade</p></dd><dt><span class="term"><code class="option">-N</code> <em class="replaceable"><code>number</code></em></span></dt><dd><p>Use this option to specify where the numbering of the references is supposed to start. The default is 1. This option comes in handy if you need to cobble together composite bibliographies or per-chapter bibliographies that still need to be numbered consecutively.</p></dd><dt><span class="term"><code class="option">-r</code></span></dt><dd><p>Use this option to request a raw instead of a cooked bibliography. Raw bibliographies are not formatted in any way and are processed with the standard DocBook or TEI stylesheets instead of with the RefDB driver files.</p></dd><dt><span class="term"><code class="option">-s</code></span></dt><dd><p>Skip the ID extraction step of runbib. You have to provide an aptly named XML file containing the requested IDs.</p></dd><dt><span class="term"><code class="option">-S</code> <em class="replaceable"><code>style</code></em></span></dt><dd><p>Specifies the bibliography style. This controls the formatting of the bibliography and the in-text citations when the document is processed.</p></dd><dt><span class="term"><code class="option">-t</code> <em class="replaceable"><code>output-type</code></em></span></dt><dd><p>Select the output type. Use <span class="emphasis"><em>db31</em></span> to generate DocBook SGML bibliographies, <span class="emphasis"><em>db31x</em></span> for DocBook XML bibliographies, <span class="emphasis"><em>teix</em></span> for TEI XML bibliographies, <span class="emphasis"><em>bibtex</em></span> for BibTeX bibliographies, and <span class="emphasis"><em>rtf</em></span> for RTF bibliographies.</p></dd><dt><span class="term">
<code class="option">-u</code> <em class="replaceable"><code>name</code></em></span></dt><dd><p>Set the username for the database access.
Note: This username need not be identical to the login name of the user. This is the username required to access the database server.</p></dd><dt><span class="term"><code class="option">-w</code> <em class="replaceable"><code>password</code></em></span></dt><dd><p>Set the password for the database access.
Note: This password need not be identical to the login password of the user. This is the password required to access the database server.</p></dd></dl></div></div><div class="refsect1"><a id="runbib-configuration"></a><h2>Configuration</h2><p>Instead of using the command-line switches, runbib can also be configured by means of the runbib configuration file. As with all refdb configuration files, you may maintain a global copy in <code class="filename">/usr/local/etc/refdb/</code> and one copy per user in <code class="envar">$HOME</code>. Keep in mind that the runbib configuration file covers only those options which are not passed to refdbib(1) as that tool has its own configuration file.</p><div class="table"><a id="idp69343264"></a><p class="title"><strong>Table 15.2. refdbjaderc</strong></p><div class="table-contents"><table class="table" summary="refdbjaderc" border="1"><colgroup><col /><col /><col /></colgroup><thead><tr><th>Variable</th><th>Default</th><th>Comment</th></tr></thead><tbody><tr><td>jade_includearg</td><td>none</td><td>Change the value of an entity declaration to include marked sections. Multiple entries are possible. These are passed as <code class="option">-i</code> options to Jade/OpenJade.</td></tr><tr><td>jadeargs</td><td>none</td><td>Set additional command line options for Jade/OpenJade. Use e.g. "-E 0" to disable the maximum error limit</td></tr><tr><td>outformat</td><td>db31</td><td>Set the default output format. Supported values are db31 (DocBook SGML 3.1 and later), db31x (DocBook XML 3.1 and later), db50x (DocBook XML 5.0 and later), teix (TEI P4), bibtex, and rtf.</td></tr></tbody></table></div></div><br class="table-break" /></div><div class="refsect1"><a id="runbib-sgml"></a><h2>SGML Output</h2><p>refdbib generates two output files in addition to the ID listing created by Jade/OpenJade. runbib creates another output file from these. Assuming you have a source file <code class="filename">foo.sgml</code> and use the bibliography style <code class="filename">J.Biol.Chem.</code> you will get:</p><div class="variablelist"><dl class="variablelist"><dt><span class="term">
<code class="filename">J.Biol.Chem.dsl</code>
</span></dt><dd><p>This is the DSSSL driver file file that encodes some additional formatting information specific for the chosen bibliography style for use in subsequent document transformations. This file will be written to the present working directory. The driver file is a dual-purpose stylesheet for HTML and printable output.</p></dd><dt><span class="term">
<code class="filename">foo.id.xml</code>
</span></dt><dd><p>This is the intermediate XML file that encodes the citations in foo.sgml.</p></dd><dt><span class="term">
<code class="filename">foo.bib.sgml</code>
</span></dt><dd><p>This is the file that holds the DocBook <code class="sgmltag-element">bibliography</code> element. You have to include this file as an external entity into your source document to integrate the bibliography into your text.</p></dd><dt><span class="term">
<code class="filename">J.Biol.Chem.css</code>
</span></dt><dd><p>This is a CSS file which contains formatting information used by the html output.</p></dd></dl></div></div><div class="refsect1"><a id="runbib-xml"></a><h2>XML Output</h2><p>refdbib again generates two output files as for the DocBook SGML output above, and we also count the ID listing created by xsltproc. However, runbib does a little post-processing, so you'll get two additional files in the end. Assuming you have a source file <code class="filename">foo.xml</code> and use the bibliography style <code class="filename">J.Biol.Chem.</code> you will get:</p><div class="variablelist"><dl class="variablelist"><dt><span class="term">
<code class="filename">J.Biol.Chem.fo.xsl</code>
</span></dt><dd><p>This is the XSL driver file used for printable output, containing additional formatting information specific for the chosen bibliography style. This file will be written to the present working directory.</p></dd><dt><span class="term">
<code class="filename">J.Biol.Chem.html.xsl</code>
</span></dt><dd><p>This is the XSL driver file used for HTML output, containing additional formatting information specific for the chosen bibliography style. This file will be written to the present working directory.</p></dd><dt><span class="term">
<code class="filename">foo.id.xml</code>
</span></dt><dd><p>This is the intermediate XML file that encodes the citations in foo.xml.</p></dd><dt><span class="term">
<code class="filename">foo.bib.xml</code>
</span></dt><dd><p>This is the file that holds the DocBook or TEI bibliography. You have to include this file as an external entity into your source document to integrate the bibliography into your text.</p></dd><dt><span class="term">
<code class="filename">J.Biol.Chem.css</code>
</span></dt><dd><p>This is a CSS file which contains formatting information used by the html or xhtml output.</p></dd></dl></div></div><div class="refsect1"><a id="runbib-bibtex"></a><h2>Bibtex Output</h2><p>refdbib creates one output file with the reference information. If your document is named <code class="filename">foo.tex</code>, <span class="command"><strong>latex</strong></span> will create a file <code class="filename">foo.aux</code> which refdbib uses as an input file. The refdbib output file will then be named <code class="filename">foo.bib</code> and can be used by <span class="command"><strong>bibtex</strong></span> as an input file.</p></div><div class="refsect1"><a id="runbib-rtf"></a><h2>RTF Output</h2><p>refdbib creates one output file with the reference information. If your document is named <code class="filename">foo.rtf</code>, <span class="command"><strong>rtfcitations</strong></span> extracts the citations and writes them into <code class="filename">foo.id.xml</code> which refdbib uses as an input file. The refdbib output file will then be named <code class="filename">foo.bib.rtf</code> and can be used by <span class="command"><strong>refdbrtf</strong></span> as an input file.</p></div><div class="refsect1"><a id="runbib-example"></a><h2>Example</h2><p>You should run this script from the directory where your document files are stored, as all output will be written to the present working directory by default.</p><p>The following command will create a DocBook SGML bibliography file together with a DSSSL stylesheet driver file for the DocBook SGML document <code class="filename">mypaper.sgml</code>. The output files are tweaked to match the citation and bibliography style of the "Journal of Biological Chemistry", which was added to the database with the name "J.Biol.Chem." previously. All references which do not contain a hard-coded database name are assumed to be in the database <code class="filename">bar</code>.</p><pre class="screen">
<code class="prompt">~$ </code>
<strong class="userinput"><code>runbib -d bar -S "J.Biol.Chem." -t db31 mypaper.sgml</code></strong>
</pre></div><div class="refsect1"><a id="runbib-files"></a><h2>Files</h2><div class="variablelist"><dl class="variablelist"><dt><span class="term"><code class="filename">PREFIX/etc/refdb/refdbibrc</code></span></dt><dd><p>The global configuration file of refdbib(1), which does most of the work of runbib.</p></dd><dt><span class="term"><code class="filename">$HOME/.refdbibrc</code></span></dt><dd><p>The user configuration file of refdbib.</p></dd></dl></div></div><div class="refsect1"><a id="runbib-see_also"></a><h2>See also</h2><p><span class="emphasis"><em>RefDB</em></span> (7),
<span class="emphasis"><em><a class="link" href="re02.html" title="refdbd">refdbd</a></em></span> (1),
<span class="emphasis"><em><a class="link" href="re20.html" title="refdbib">refdbib</a></em></span> (1),
<span class="emphasis"><em><a class="link" href="re21.html" title="refdbnd">refdbnd</a></em></span> (1),
<span class="emphasis"><em><a class="link" href="re06.html" title="refdba">refdba</a></em></span> (1),
<span class="emphasis"><em><a class="link" href="re11.html" title="refdbc">refdbc</a></em></span> (1).</p><p><span class="emphasis"><em>RefDB manual (local copy) </em></span> PREFIX/share/doc/refdb-<version>/refdb-manual/index.html</p><p><span class="emphasis"><em>RefDB manual (web) </em></span> <<a class="ulink" href="http://refdb.sourceforge.net/manual/index.html" target="_top">http://refdb.sourceforge.net/manual/index.html</a>></p><p><span class="emphasis"><em>RefDB on the web </em></span> <<a class="ulink" href="http://refdb.sourceforge.net/" target="_top">http://refdb.sourceforge.net/</a>></p></div><div class="refsect1"><a id="runbib-author"></a><h2>Author</h2><p>runbib was written by Markus Hoenicka <markus@mhoenicka.de>.</p></div></div><div class="navfooter"><hr /><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="re21.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="ch15.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="re23.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">refdbnd </td><td width="20%" align="center"><a accesskey="h" href="index.html">Home</a></td><td width="40%" align="right" valign="top"> runbib-missing</td></tr></table></div></body></html>
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