[DRE-commits] [SCM] ruby-bio.git branch, master, updated. upstream/1.4.1-3-g73f2eca
Lucas Nussbaum
lucas at lucas-nussbaum.net
Fri Jul 29 14:00:49 UTC 2011
The following commit has been merged in the master branch:
commit 73f2eca57068b19cadcc9f2fca0209857cb15b09
Author: Lucas Nussbaum <lucas at lucas-nussbaum.net>
Date: Thu Jul 28 18:30:49 2011 +0200
continue packaging
diff --git a/debian/br_biofetch.rb.sgml b/debian/br_biofetch.rb.sgml
new file mode 100644
index 0000000..33d3395
--- /dev/null
+++ b/debian/br_biofetch.rb.sgml
@@ -0,0 +1,182 @@
+<!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 at 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>
+
+<!-- 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
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+
diff --git a/debian/br_bioflat.rb.sgml b/debian/br_bioflat.rb.sgml
new file mode 100644
index 0000000..031836f
--- /dev/null
+++ b/debian/br_bioflat.rb.sgml
@@ -0,0 +1,256 @@
+<!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 at 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
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+
diff --git a/debian/br_biogetseq.rb.sgml b/debian/br_biogetseq.rb.sgml
new file mode 100644
index 0000000..aed8965
--- /dev/null
+++ b/debian/br_biogetseq.rb.sgml
@@ -0,0 +1,144 @@
+<!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 at 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
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+
diff --git a/debian/br_pmfetch.rb.sgml b/debian/br_pmfetch.rb.sgml
new file mode 100644
index 0000000..168d566
--- /dev/null
+++ b/debian/br_pmfetch.rb.sgml
@@ -0,0 +1,288 @@
+<!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 at 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>
+ <term>
+ <option>--reldate</option>
+ </term>
+ <listitem>
+ <para>Search articles published within recent # of days.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>--mindate</option>
+ </term>
+ <listitem>
+ <para>Search articles published after the date YYYY/MM/DD.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>--maxdate</option>
+ </term>
+ <listitem>
+ <para>Search articles published before the date YYYY/MM/DD.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>--help</option>
+ </term>
+ <listitem>
+ <para>Output help and then exit.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>--examples</option>
+ </term>
+ <listitem>
+ <para>Output example usages and then exit.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>--version</option>
+ </term>
+ <listitem>
+ <para>Output version number and then exit.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+ <refsect1>
+ <title>SEE ALSO</title>
+
+ <para> The following pages have information on the PubMed search
+ options: http://www.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html
+ http://www.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html</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>
+
+<!-- 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
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+
diff --git a/debian/changelog b/debian/changelog
index 4051013..d9c4669 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,10 +1,9 @@
-ruby-bio (1.4.1-2) UNRELEASED; urgency=low
+ruby-bio (1.4.1-2) unstable; urgency=low
- TODO: tests need ruby-soap4r (not packaged yet for ruby1.9.1)
- * Switch to gem2deb-based packaging. Rename package and introduce
+ * Switch to gem2deb packaging. Rename binary and source package, introduce
transitional packages.
- -- Lucas Nussbaum <lucas at debian.org> Wed, 15 Jun 2011 21:47:52 +0200
+ -- Lucas Nussbaum <lucas at debian.org> Thu, 28 Jul 2011 17:25:55 +0200
bioruby (1.4.1-1) unstable; urgency=low
diff --git a/debian/control b/debian/control
index 154fae5..c90bb4c 100644
--- a/debian/control
+++ b/debian/control
@@ -9,7 +9,7 @@ Build-Depends-Indep: docbook-to-man, rdtool
Standards-Version: 3.9.2
Vcs-Git: git://git.debian.org/pkg-ruby-extras/ruby-bio.git
Vcs-Browser: http://git.debian.org/?p=pkg-ruby-extras/ruby-bio.git;a=summary
-Homepage: http://bioruby.org/
+Homepage: http://www.bioruby.org/
XS-Ruby-Versions: all
Package: ruby-bio
@@ -19,9 +19,9 @@ Depends: ${shlibs:Depends}, ${misc:Depends}, ruby | ruby-interpreter
Recommends: blast2, hmmer, mafft, muscle, probcons, sim4, t-coffee
Suggests: clustalw, emboss
Replaces: libbio-ruby1.8 (<< 1.4.1-2~), libbio-ruby (<< 1.4.1-2~)
-Conflicts: libbio-ruby1.8 (<< 1.4.1-2~), libbio-ruby (<< 1.4.1-2~)
+Breaks: libbio-ruby1.8 (<< 1.4.1-2~), libbio-ruby (<< 1.4.1-2~)
Provides: libbio-ruby1.8, libbio-ruby
-Description: bioruby tools for computational molecular biology
+Description: Ruby tools for computational molecular biology
BioRuby project aims to implement an integrated environment for
Bioinformatics with Ruby language. Design philosophy of the BioRuby library
is KISS (keep it simple, stupid) to maximize the usability and the
diff --git a/debian/copyright b/debian/copyright
index c7fc83a..084cb81 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,75 +1,72 @@
-This package was debianized by David Nusinow <dnusinow at debian.org> on
-Mon, 31 Jan 2005 11:11:55 -0500.
-
-It was downloaded from http://www.bioruby.org
-
-Copyright: KATAYAMA Toshiaki <k at bioruby.org>
-
-Upstream Authors: * KATAYAMA Toshiaki <k at bioruby.org>, project leader
- * Yoshinori K. Okuji <okuji at enbug.org>
- * Mitsuteru C. Nakao <n at bioruby.org>
- * KAWASHIMA Shuichi <s at bioruby.org>
- * GOTO Naohisa <ng at bioruby.org>
-
-License:
-
-This library is distributed under the same terms as ruby. As such, it may
-be distributed either under the terms of the GPL or the conditions below:
-
- 1. You may make and give away verbatim copies of the source form of the
- software without restriction, provided that you duplicate all of the
- original copyright notices and associated disclaimers.
-
- 2. You may modify your copy of the software in any way, provided that
- you do at least ONE of the following:
-
- a) place your modifications in the Public Domain or otherwise
- make them Freely Available, such as by posting said
- modifications to Usenet or an equivalent medium, or by allowing
- the author to include your modifications in the software.
-
- b) use the modified software only within your corporation or
- organization.
-
- c) rename any non-standard executables so the names do not conflict
- with standard executables, which must also be provided.
-
- d) make other distribution arrangements with the author.
-
- 3. You may distribute the software in object code or executable
- form, provided that you do at least ONE of the following:
-
- a) distribute the executables and library files of the software,
- together with instructions (in the manual page or equivalent)
- on where to get the original distribution.
-
- b) accompany the distribution with the machine-readable source of
- the software.
-
- c) give non-standard executables non-standard names, with
- instructions on where to get the original software distribution.
-
- d) make other distribution arrangements with the author.
-
- 4. You may modify and include the part of the software into any other
- software (possibly commercial). But some files in the distribution
- are not written by the author, so that they are not under this terms.
- They are gc.c(partly), utils.c(partly), regex.[ch], fnmatch.[ch],
- glob.c, st.[ch] and some files under the ./missing directory. See
- each file for the copying condition.
-
- 5. The scripts and library files supplied as input to or produced as
- output from the software do not automatically fall under the
- copyright of the software, but belong to whomever generated them,
- and may be sold commercially, and may be aggregated with this
- software.
-
- 6. THIS SOFTWARE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR
- IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
- WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR
- PURPOSE.
-
---
-On Debian GNU/Linux systems, the complete text of the GNU General
-Public License can be found in `/usr/share/common-licenses/GPL'.
-
+# DEP5 version of the Copyright file in the bioruby source package
+Format: http://svn.debian.org/wsvn/dep/web/deps/dep5.mdwn?op=file&rev=173
+Upstream-Name: bio
+Source: http://www.bioruby.org/
+
+Files: *
+Copyright: Copyright Toshiaki Katayama <k at bioruby.org>
+License: GPL-2 or Ruby
+ BioRuby is copyrighted free software by Toshiaki Katayama <k at bioruby.org>.
+ You can redistribute it and/or modify it under either the terms of the GPL
+ version 2 (see the file GPL), or the conditions below:
+
+ 1. You may make and give away verbatim copies of the source form of the
+ software without restriction, provided that you duplicate all of the
+ original copyright notices and associated disclaimers.
+
+ 2. You may modify your copy of the software in any way, provided that
+ you do at least ONE of the following:
+
+ a) place your modifications in the Public Domain or otherwise
+ make them Freely Available, such as by posting said
+ modifications to Usenet or an equivalent medium, or by allowing
+ the author to include your modifications in the software.
+
+ b) use the modified software only within your corporation or
+ organization.
+
+ c) give non-standard binaries non-standard names, with
+ instructions on where to get the original software distribution.
+
+ d) make other distribution arrangements with the author.
+
+ 3. You may distribute the software in object code or binary form,
+ provided that you do at least ONE of the following:
+
+ a) distribute the binaries and library files of the software,
+ together with instructions (in the manual page or equivalent)
+ on where to get the original distribution.
+
+ b) accompany the distribution with the machine-readable source of
+ the software.
+
+ c) give non-standard binaries non-standard names, with
+ instructions on where to get the original software distribution.
+
+ d) make other distribution arrangements with the author.
+
+ 4. You may modify and include the part of the software into any other
+ software (possibly commercial). But some files in the distribution
+ are not written by the author, so that they are not under these terms.
+
+ For the list of those files and their copying conditions, see the
+ file LEGAL.
+
+ 5. The scripts and library files supplied as input to or produced as
+ output from the software do not automatically fall under the
+ copyright of the software, but belong to whomever generated them,
+ and may be sold commercially, and may be aggregated with this
+ software.
+
+ 6. THIS SOFTWARE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR
+ IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ PURPOSE.
+
+ On Debian systems, the full text of the GNU General Public
+ License version 2 can be found in the file
+ `/usr/share/common-licenses/GPL-2'.
+
+Files: debian/*
+Copyright: Copyright 2011 Lucas Nussbaum <lucas at debian.org>
+License: same as upstream
diff --git a/debian/patches/disable-test-soap.patch b/debian/patches/disable-test-soap.patch
new file mode 100644
index 0000000..044d1b2
--- /dev/null
+++ b/debian/patches/disable-test-soap.patch
@@ -0,0 +1,56 @@
+--- a/test/functional/bio/io/test_soapwsdl.rb
++++ /dev/null
+@@ -1,53 +0,0 @@
+-#
+-# test/functional/bio/io/test_soapwsdl.rb - Functional test for SOAP/WSDL
+-#
+-# Copyright:: Copyright (C) 2005,2007
+-# Mitsuteru C. Nakao <n at bioruby.org>
+-# License:: The Ruby License
+-#
+-# $Id:$
+-#
+-
+-# loading helper routine for testing bioruby
+-require 'pathname'
+-load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+- 'bioruby_test_helper.rb')).cleanpath.to_s
+-
+-# libraries needed for the tests
+-require 'test/unit'
+-require 'bio/io/soapwsdl'
+-
+-module Bio
+-
+-class FuncTestSOAPWSDL < Test::Unit::TestCase
+-
+- def setup
+- @wsdl = 'http://www.ebi.ac.uk/xembl/XEMBL.wsdl'
+- @obj = Bio::SOAPWSDL.new(@wsdl)
+- end
+-
+- def test_wsdl
+- assert_equal(@wsdl, @obj.wsdl)
+- end
+-
+- def test_set_wsdl
+- @obj.wsdl = 'http://soap.genome.jp/KEGG.wsdl'
+- assert_equal('http://soap.genome.jp/KEGG.wsdl', @obj.wsdl)
+- end
+-
+- def test_log
+- assert_equal(nil, @obj.log)
+- end
+-
+- def test_set_log
+- require 'stringio'
+- io = StringIO.new
+- @obj.log = io
+-
+- assert_equal(StringIO, @obj.log.class)
+- end
+-
+-end
+-
+-end
+-
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..b427531
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+disable-test-soap.patch
diff --git a/debian/ruby-tests.rb b/debian/ruby-tests.rb
index ff709fe..bc13ba3 100644
--- a/debian/ruby-tests.rb
+++ b/debian/ruby-tests.rb
@@ -1,2 +1,6 @@
+if RUBY_VERSION >= '1.9.1'
+ Encoding.default_external = "UTF-8"
+end
+
$: << 'lib' << 'test' << '.'
Dir['{spec,test}/**/test_*.rb'].each { |f| require f }
diff --git a/debian/rules b/debian/rules
index dabd241..87c4312 100755
--- a/debian/rules
+++ b/debian/rules
@@ -24,3 +24,10 @@ override_dh_auto_build:
override_dh_auto_clean:
dh_auto_clean
rm -f br_biofetch.1 br_bioflat.1 br_biogetseq.1 br_pmfetch.1
+
+override_dh_auto_install:
+ dh_auto_install
+ for FILE in `ls debian/ruby-bio/usr/bin/*rb`; do \
+ BINNAME=$$(echo $$FILE | sed 's/\.rb$$//'); \
+ mv $$FILE $$BINNAME; \
+ done
--
ruby-bio.git
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