Commit 73f2eca5 authored by Lucas Nussbaum's avatar Lucas Nussbaum

continue packaging

parent 663c2caa
<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
<!-- Process this file with docbook-to-man to generate an nroff manual
page: `docbook-to-man manpage.sgml > manpage.1'. You may view
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less'. A typical entry in a Makefile or Makefile.am is:
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<!-- Fill in your name for FIRSTNAME and SURNAME. -->
<!ENTITY dhfirstname "<firstname>David</firstname>">
<!ENTITY dhsurname "<surname>Nusinow</surname>">
<!-- Please adjust the date whenever revising the manpage. -->
<!ENTITY dhdate "<date>January 31, 2005</date>">
<!-- SECTION should be 1-8, maybe w/ subsection other parameters are
allowed: see man(7), man(1). -->
<!ENTITY dhsection "<manvolnum>1</manvolnum>">
<!ENTITY dhemail "<email>dnusinow@debian.org</email>">
<!ENTITY dhusername "David Nusinow">
<!ENTITY dhucpackage "<refentrytitle>BIORUBY</refentrytitle>">
<!ENTITY dhpackage "br_biofetch.rb">
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
]>
<refentry>
<refentryinfo>
<address>
&dhemail;
</address>
<author>
&dhfirstname;
&dhsurname;
</author>
<copyright>
<year>2005</year>
<holder>&dhusername;</holder>
</copyright>
&dhdate;
</refentryinfo>
<refmeta>
&dhucpackage;
&dhsection;
</refmeta>
<refnamediv>
<refname>&dhpackage;</refname>
<refpurpose>biofetch client</refpurpose>
</refnamediv>
<refsynopsisdiv>
<cmdsynopsis>
<command>&dhpackage;</command>
<arg><option>-s</option> <replaceable>server</replaceable></arg>
<arg><replaceable>db</replaceable></arg>
<arg><replaceable>id</replaceable></arg>
<arg><option><replaceable>style</replaceable></option></arg>
<arg><option><replaceable>format</replaceable></option></arg>
</cmdsynopsis>
</refsynopsisdiv>
<refsect1>
<title>DESCRIPTION</title>
<para>This manual page documents briefly the
<command>&dhpackage;</command>.</para>
<para><command>&dhpackage;</command> is a very simple biofetch client. You
can connect to a biofetch server and retrieve database entries including
sequence information.</para>
</refsect1>
<refsect1>
<title>OPTIONS</title>
<variablelist>
<varlistentry>
<term><option>-s</option>
</term>
<listitem>
<para>Specify the URL of the BioFetch CGI (default is http://bioruby.org/cgi-bin/biofetch.rb) </para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-e</option>
</term>
<listitem>
<para>Use the EBI server at http://www.ebi.ac.uk/cgi-bin/dbfetch</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-r</option>
</term>
<listitem>
<para>Use the BioRuby server at http://bioruby.org/cgi-bin/biofetch.rb</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>db</option>
</term>
<listitem>
<para>Database name. This includes options like refseq, genbank,
embl, swissprot, etc. This option depends on which biofetch server
you are using.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>id</option>
</term>
<listitem>
<para>entry id</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>style</option>
</term>
<listitem>
<para>\'raw\' or \'html\' (default is \'raw\')</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>format</option>
</term>
<listitem>
<para>Output format ('default, 'fasta', 'etc')</para>
</listitem>
</varlistentry>
</variablelist>
</refsect1>
<refsect1>
<title>SEE ALSO</title>
<para>bar (1), baz (1).</para>
</refsect1>
<refsect1>
<title>AUTHOR</title>
<para>This manual page was written by &dhusername; &dhemail; for
the &debian; system (but may be used by others). Permission is
granted to copy, distribute and/or modify this document under
the terms of the &gnu; General Public License, Version 2 any
later version published by the Free Software Foundation.
</para>
<para>
On Debian systems, the complete text of the GNU General Public
License can be found in /usr/share/common-licenses/GPL.
</para>
</refsect1>
</refentry>
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Local variables:
mode: sgml
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<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
<!-- Process this file with docbook-to-man to generate an nroff manual
page: `docbook-to-man manpage.sgml > manpage.1'. You may view
the manual page with: `docbook-to-man manpage.sgml | nroff -man |
less'. A typical entry in a Makefile or Makefile.am is:
manpage.1: manpage.sgml
docbook-to-man $< > $@
The docbook-to-man binary is found in the docbook-to-man package.
Please remember that if you create the nroff version in one of the
debian/rules file targets (such as build), you will need to include
docbook-to-man in your Build-Depends control field.
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<!-- Fill in your name for FIRSTNAME and SURNAME. -->
<!ENTITY dhfirstname "<firstname>David</firstname>">
<!ENTITY dhsurname "<surname>Nusinow</surname>">
<!-- Please adjust the date whenever revising the manpage. -->
<!ENTITY dhdate "<date>January 31, 2005</date>">
<!-- SECTION should be 1-8, maybe w/ subsection other parameters are
allowed: see man(7), man(1). -->
<!ENTITY dhsection "<manvolnum>1</manvolnum>">
<!ENTITY dhemail "<email>dnusinow@debian.org</email>">
<!ENTITY dhusername "David Nusinow">
<!ENTITY dhucpackage "<refentrytitle>BIORUBY</refentrytitle>">
<!ENTITY dhpackage "br_bioflat.rb">
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
]>
<refentry>
<refentryinfo>
<address>
&dhemail;
</address>
<author>
&dhfirstname;
&dhsurname;
</author>
<copyright>
<year>2005</year>
<holder>&dhusername;</holder>
</copyright>
&dhdate;
</refentryinfo>
<refmeta>
&dhucpackage;
&dhsection;
</refmeta>
<refnamediv>
<refname>&dhpackage;</refname>
<refpurpose>OBDA flat file indexer</refpurpose>
</refnamediv>
<refsynopsisdiv>
<para>Search:</para>
<cmdsynopsis>
<command>&dhpackage;</command>
<arg><option>--search</option></arg>
<arg><option>options...</option></arg>
</cmdsynopsis>
<cmdsynopsis>
<command>&dhpackage;</command>
<arg><option>--search</option></arg>
<arg>--location <replaceable>DIR</replaceable></arg>
<arg>--dbname <replaceable>DBNAME</replaceable></arg>
<arg><option>options...</option></arg>
<arg><replaceable>KEYWORDS</replaceable></arg>
</cmdsynopsis>
<para>Create index:</para>
<cmdsynopsis>
<command>&dhpackage;</command>
<arg><option>--create</option></arg>
<arg><option>--location <replaceable>DIR</replaceable></option></arg>
<arg><option>--dbname <replaceable>DBNAME</replaceable></option></arg>
<arg><option>--format <replaceable>genbank|embl|fasta</replaceable></option></arg>
<arg><option>options...</option></arg>
<arg><option>--files <replaceable>FILES...</replaceable></option></arg>
</cmdsynopsis>
<para>Update index:</para>
<cmdsynopsis>
<command>&dhpackage;</command>
<arg><option>--update</option></arg>
<arg><option>--location <replaceable>DIR</replaceable></option></arg>
<arg><option>--dbname <replaceable>DBNAME</replaceable></option></arg>
<arg><option>options...</option></arg>
<arg><option>--files <replaceable>FILES...</replaceable></option></arg>
</cmdsynopsis>
<para>Show namespaces:</para>
<cmdsynopsis>
<command>&dhpackage;</command>
<arg><option>--show-namespaces</option></arg>
<arg><option>--location <replaceable>DIR</replaceable></option></arg>
<arg><option>--dbname <replaceable>DBNAME</replaceable></option></arg>
<arg><option><replaceable>DIR/DBNAME</replaceable></option></arg>
</cmdsynopsis>
<cmdsynopsis>
<command>&dhpackage;</command>
<arg><option>--show-namespaces</option></arg>
<arg><option>--format=<replaceable>CLASS</replaceable></option></arg>
</cmdsynopsis>
<cmdsynopsis>
<command>&dhpackage;</command>
<arg><option>--show-namespaces</option></arg>
<arg><option>--files <replaceable>file</replaceable></option></arg>
</cmdsynopsis>
</refsynopsisdiv>
<refsect1>
<title>DESCRIPTION</title>
<para>This manual page documents briefly the
<command>&dhpackage;</command>.</para>
<para><command>&dhpackage;</command> is an OBDA flat file indexer.</para>
</refsect1>
<refsect1>
<title>OPTIONS</title>
<variablelist>
<varlistentry>
<term><option>--search</option>
</term>
<listitem>
<para>Search a database for keywords.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>--namespace</option>
<option>--name</option>
</term>
<listitem>
<para>Only valid with the --search option. Set the search namespace.
You can set this option multiple times to specify more than one
namespace.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>--create</option>
</term>
<listitem>
<para>Create an index.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>--location</option>
</term>
<listitem>
<para>Specify the directory.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>--dbname</option>
</term>
<listitem>
<para>Specify the name of the database.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>--primary</option>
<option>--secondary</option>
</term>
<listitem>
<para>Set the primary and secondarynamespace of the index. Default
primary/secondary namespaces depend on the format of the flatfiles.
Only valid with the --create option.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>--add-secondary</option>
</term>
<listitem>
<para>Add secondary namespaces to the default specification. You can
use this option many times. Only valid with the --create option.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>--update</option>
</term>
<listitem>
<para>Update an index</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>--sort</option>
</term>
<listitem>
<para>Sort an index. You can set this to a path to an external
sorting program, or BUILTIN to use the builtin sort module. This
option is only valid with --create (or --update) and --type flat
options.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>--renew</option>
</term>
<listitem>
<para>Re-read all flatfiles and update whole index. This option is
only valid with the --update option.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>--show-namespaces</option>
</term>
<listitem>
<para>Display the namespaces for an index file.</para>
</listitem>
</varlistentry>
</variablelist>
</refsect1>
<refsect1>
<title>AUTHOR</title>
<para>This manual page was written by &dhusername; &dhemail; for
the &debian; system (but may be used by others). Permission is
granted to copy, distribute and/or modify this document under
the terms of the &gnu; General Public License, Version 2 any
later version published by the Free Software Foundation.
</para>
<para>
On Debian systems, the complete text of the GNU General Public
License can be found in /usr/share/common-licenses/GPL.
</para>
</refsect1>
</refentry>
<!-- Keep this comment at the end of the file
Local variables:
mode: sgml
sgml-omittag:t
sgml-shorttag:t
sgml-minimize-attributes:nil
sgml-always-quote-attributes:t
sgml-indent-step:2
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End:
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<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
<!-- Process this file with docbook-to-man to generate an nroff manual
page: `docbook-to-man manpage.sgml > manpage.1'. You may view
the manual page with: `docbook-to-man manpage.sgml | nroff -man |
less'. A typical entry in a Makefile or Makefile.am is:
manpage.1: manpage.sgml
docbook-to-man $< > $@
The docbook-to-man binary is found in the docbook-to-man package.
Please remember that if you create the nroff version in one of the
debian/rules file targets (such as build), you will need to include
docbook-to-man in your Build-Depends control field.
-->
<!-- Fill in your name for FIRSTNAME and SURNAME. -->
<!ENTITY dhfirstname "<firstname>David</firstname>">
<!ENTITY dhsurname "<surname>Nusinow</surname>">
<!-- Please adjust the date whenever revising the manpage. -->
<!ENTITY dhdate "<date>January 31, 2005</date>">
<!-- SECTION should be 1-8, maybe w/ subsection other parameters are
allowed: see man(7), man(1). -->
<!ENTITY dhsection "<manvolnum>1</manvolnum>">
<!ENTITY dhemail "<email>dnusinow@debian.org</email>">
<!ENTITY dhusername "David Nusinow">
<!ENTITY dhucpackage "<refentrytitle>BIORUBY</refentrytitle>">
<!ENTITY dhpackage "br_biogetseq">
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
]>
<refentry>
<refentryinfo>
<address>
&dhemail;
</address>
<author>
&dhfirstname;
&dhsurname;
</author>
<copyright>
<year>2005</year>
<holder>&dhusername;</holder>
</copyright>
&dhdate;
</refentryinfo>
<refmeta>
&dhucpackage;
&dhsection;
</refmeta>
<refnamediv>
<refname>&dhpackage;</refname>
<refpurpose>ODBA Sequence Retrieval</refpurpose>
</refnamediv>
<refsynopsisdiv>
<cmdsynopsis>
<command>&dhpackage;</command>
<arg><option>--dbname <replaceable>DBNAME</replaceable></option></arg>
<arg><option>--namespace <replaceable>NAMESPACE</replaceable></option></arg>
<arg><option>entry_id <replaceable>ENTRY_ID</replaceable></option></arg>
</cmdsynopsis>
</refsynopsisdiv>
<refsect1>
<title>DESCRIPTION</title>
<para>This manual page documents briefly the
<command>&dhpackage;</command>.</para>
<para><command>&dhpackage;</command> is an ODBC sequence retrieval program.
Simply point it at the database of interest, with an optional namespace,
and give it the sequence id that you want, and it will retrieve it.</para>
</refsect1>
<refsect1>
<title>OPTIONS</title>
<variablelist>
<varlistentry>
<term><option>--dbname</option>
</term>
<listitem>
<para>Specify the database to query (required).</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>--namespace</option>
</term>
<listitem>
<para>Specify the namespace to query.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>entry_id</option>
</term>
<listitem>
<para>Specify the ID of the sequence to be retrieved.</para>
</listitem>
</varlistentry>
</variablelist>
</refsect1>
<refsect1>
<title>AUTHOR</title>
<para>This manual page was written by &dhusername; &dhemail; for
the &debian; system (but may be used by others). Permission is
granted to copy, distribute and/or modify this document under
the terms of the &gnu; General Public License, Version 2 any
later version published by the Free Software Foundation.
</para>
<para>
On Debian systems, the complete text of the GNU General Public
License can be found in /usr/share/common-licenses/GPL.
</para>
</refsect1>
</refentry>
<!-- Keep this comment at the end of the file
Local variables:
mode: sgml
sgml-omittag:t
sgml-shorttag:t
sgml-minimize-attributes:nil
sgml-always-quote-attributes:t
sgml-indent-step:2
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End:
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<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
<!-- Process this file with docbook-to-man to generate an nroff manual
page: `docbook-to-man manpage.sgml > manpage.1'. You may view
the manual page with: `docbook-to-man manpage.sgml | nroff -man |
less'. A typical entry in a Makefile or Makefile.am is:
manpage.1: manpage.sgml
docbook-to-man $< > $@
The docbook-to-man binary is found in the docbook-to-man package.
Please remember that if you create the nroff version in one of the
debian/rules file targets (such as build), you will need to include
docbook-to-man in your Build-Depends control field.
-->
<!-- Fill in your name for FIRSTNAME and SURNAME. -->
<!ENTITY dhfirstname "<firstname>David</firstname>">
<!ENTITY dhsurname "<surname>Nusinow</surname>">
<!-- Please adjust the date whenever revising the manpage. -->
<!ENTITY dhdate "<date>January 31, 2005</date>">
<!-- SECTION should be 1-8, maybe w/ subsection other parameters are
allowed: see man(7), man(1). -->
<!ENTITY dhsection "<manvolnum>1</manvolnum>">
<!ENTITY dhemail "<email>dnusinow@debian.org</email>">
<!ENTITY dhusername "David Nusinow">
<!ENTITY dhucpackage "<refentrytitle>BIORUBY</refentrytitle>">
<!ENTITY dhpackage "br_pmfetch">
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
]>
<refentry>
<refentryinfo>
<address>
&dhemail;
</address>
<author>
&dhfirstname;
&dhsurname;
</author>
<copyright>
<year>2005</year>
<holder>&dhusername;</holder>
</copyright>
&dhdate;
</refentryinfo>
<refmeta>
&dhucpackage;
&dhsection;
</refmeta>
<refnamediv>
<refname>&dhpackage;</refname>
<refpurpose>PubMed Client</refpurpose>
</refnamediv>
<refsynopsisdiv>
<cmdsynopsis>
<command>&dhpackage;</command>
<arg><option><replaceable>options...</replaceable></option></arg>
<arg>"query string"</arg>
</cmdsynopsis>
<cmdsynopsis>
<command>&dhpackage;</command>
<arg><option>--query<replaceable>"query string"</replaceable></option></arg>
<arg><option><replaceable>other options...</replaceable></option></arg>
</cmdsynopsis>
</refsynopsisdiv>
<refsect1>
<title>DESCRIPTION</title>
<para>This manual page documents briefly the
<command>&dhpackage;</command>.</para>
<para><command>&dhpackage;</command> is a command line program to query
PubMed. It can take a variety of options (documented below) to restrict
your search query, which is specified by the query string.</para>
</refsect1>
<refsect1>
<title>OPTIONS</title>
<variablelist>
<varlistentry>
<term><option>-q</option>
<option>--query</option>
</term>
<listitem>
<para>Query string for PubMed search.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-t</option>
<option>--title</option>
</term>
<listitem>
<para>Title of the article to search.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-j</option>
<option>--journal</option>
</term>
<listitem>
<para>Journal title to search.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-v</option>
<option>--volume</option>
</term>
<listitem>
<para>Journal volume to search.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-i</option>
<option>--issue</option>
</term>
<listitem>
<para>Journal issue to search.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-p</option>
<option>--page</option>
</term>
<listitem>
<para>First page number of the article to search.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-a</option>
<option>--author</option>
</term>
<listitem>
<para>Author name to search.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-m</option>
<option>--mesh</option>
</term>
<listitem>
<para>MeSH term to search.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-f</option>
<option>--format</option>
</term>
<listitem>
<para>Summary output format. Options are endnote, medline, bibitem,
bibtex, report, abstract nature, science, genome_res, genome_biol,
nar, current, trends, cell.</para>
</listitem>
</varlistentry>
<varlistentry>
<term>
<option>--pmidlist</option>
</term>
<listitem>
<para>Output only a list of PudMed IDs.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-n</option>
<option>--retmax</option>
</term>
<listitem>
<para>Number of articles to retrieve at the maximum.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-N</option>
<option>--retstart</option>
</term>
<listitem>
<para>Starting number of articles to retrieve.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-s</option>
<option>--sort</option>
</term>
<listitem>
<para>Sort method for the summary output. Options are author,
journal, pub+date.</para>
</listitem>
</varlistentry>
<varlistentry>