[med-svn] r4140 - in trunk/packages: . bioruby bioruby/trunk bioruby/trunk/debian phylip/trunk/debian/patches
Andreas Tille
tille at alioth.debian.org
Sun Oct 4 06:59:30 UTC 2009
Author: tille
Date: 2009-10-04 06:59:28 +0000 (Sun, 04 Oct 2009)
New Revision: 4140
Added:
trunk/packages/bioruby/
trunk/packages/bioruby/tags/
trunk/packages/bioruby/trunk/
trunk/packages/bioruby/trunk/debian/
trunk/packages/bioruby/trunk/debian/br_biofetch.rb.sgml
trunk/packages/bioruby/trunk/debian/br_bioflat.rb.sgml
trunk/packages/bioruby/trunk/debian/br_biogetseq.rb.sgml
trunk/packages/bioruby/trunk/debian/br_pmfetch.rb.sgml
trunk/packages/bioruby/trunk/debian/changelog
trunk/packages/bioruby/trunk/debian/compat
trunk/packages/bioruby/trunk/debian/control
trunk/packages/bioruby/trunk/debian/copyright
trunk/packages/bioruby/trunk/debian/docs
trunk/packages/bioruby/trunk/debian/rules
trunk/packages/bioruby/trunk/debian/watch
Modified:
trunk/packages/phylip/trunk/debian/patches/series
Log:
Inject current status of BioRuby
Added: trunk/packages/bioruby/trunk/debian/br_biofetch.rb.sgml
===================================================================
--- trunk/packages/bioruby/trunk/debian/br_biofetch.rb.sgml (rev 0)
+++ trunk/packages/bioruby/trunk/debian/br_biofetch.rb.sgml 2009-10-04 06:59:28 UTC (rev 4140)
@@ -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:
+-->
+
+
Added: trunk/packages/bioruby/trunk/debian/br_bioflat.rb.sgml
===================================================================
--- trunk/packages/bioruby/trunk/debian/br_bioflat.rb.sgml (rev 0)
+++ trunk/packages/bioruby/trunk/debian/br_bioflat.rb.sgml 2009-10-04 06:59:28 UTC (rev 4140)
@@ -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:
+-->
+
+
Added: trunk/packages/bioruby/trunk/debian/br_biogetseq.rb.sgml
===================================================================
--- trunk/packages/bioruby/trunk/debian/br_biogetseq.rb.sgml (rev 0)
+++ trunk/packages/bioruby/trunk/debian/br_biogetseq.rb.sgml 2009-10-04 06:59:28 UTC (rev 4140)
@@ -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:
+-->
+
+
Added: trunk/packages/bioruby/trunk/debian/br_pmfetch.rb.sgml
===================================================================
--- trunk/packages/bioruby/trunk/debian/br_pmfetch.rb.sgml (rev 0)
+++ trunk/packages/bioruby/trunk/debian/br_pmfetch.rb.sgml 2009-10-04 06:59:28 UTC (rev 4140)
@@ -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:
+-->
+
+
Added: trunk/packages/bioruby/trunk/debian/changelog
===================================================================
--- trunk/packages/bioruby/trunk/debian/changelog (rev 0)
+++ trunk/packages/bioruby/trunk/debian/changelog 2009-10-04 06:59:28 UTC (rev 4140)
@@ -0,0 +1,90 @@
+bioruby (1.1.0-1) unstable; urgency=low
+
+ * New upstream version
+ + Bioruby is now distributed under the same terms as ruby itself.
+ This gives you the option of using the GPL or a similar copyleft
+ license. See /usr/share/doc/libbio-ruby/copyright for details on the
+ alternate license.
+ + Lots of new and obsolete classes, see the upstream changelog for details
+ + BioRuby shell rewritten to utilize the rails generators
+ + Many bugfixes
+ * Re-work build system to utilize install.rb instead of my custom rules file
+ + Enable unit tests in the build
+ + Don't hardcode the binary names when hacking off the .rb suffix. Use
+ wildcards and a for loop to rename them
+ + Remove the libbio-ruby1.8.dirs file. The directories get installed by
+ the install.rb now
+ + The docs are built by install.rb now, so don't do custom stuff for them
+ in debian/rules
+ + Move building the manpages to the build-stamp target, rather than the
+ build target
+ + Add ruby to build-depends
+
+ -- David Nusinow <dnusinow at debian.org> Sun, 22 Jul 2007 18:42:39 -0400
+
+bioruby (1.0.0-1) unstable; urgency=low
+
+ * New upstream version
+ * Add the bioruby shell program
+ * Add the Changes-0.7.html doc describing updates since 0.6.x
+ * Bump standards version to 3.7.2.0. No changes needed.
+ * Bump debhelper compat to 5
+ * Move debhelper to build-depends from build-depends-indep
+
+ -- David Nusinow <dnusinow at debian.org> Thu, 17 Aug 2006 00:28:21 +0000
+
+bioruby (0.6.4-1) unstable; urgency=low
+
+ * New upstream release
+ + siRNA designer class is contributed by Itoshi Nikaido.
+ (lib/bio/util/sirna.rb)
+ + fastacmd wrapper is contributed by Shinji Shigenobu.
+ (lib/bio/io/fastacmd.rb)
+ + bl2seq parser is contributed by Tomoaki Nishiyama.
+ (lib/bio/appl/bl2seq/report.rb)
+ + new application execution factory is provided.
+ (lib/bio/command.rb)
+ + FlatFile class can accept Blast results, Spidey, Blat, Sim4 and some
+ KEGG formats (KO, GLYCAN, REACTION)
+ + some methods are added to SPTr class proposed by Luca Pireddu.
+ (lib/bio/db/embl/sptr.rb)
+ + external2go parser is added. (lib/bio/db/go.rb)
+ + improved amino/nucleic data classes to have some handy methods.
+ (lib/bio/data/)
+ + fixed hmmer parser (by Masashi Fujita) and remote execution of blast and
+ fasta using GenomeNet.
+ + some English documentations are added. (doc/)
+ * Re-organize debian/rules handling of docs
+ + Ship new English tutorial and KEGG_API. These are turned to html with rd2
+ + Put document building commands in the build target instead of configure
+ + Add commands to remove generated documents in the clean target
+ + Put package building commands in binary-indep where they belong
+ * Add build-dependency on rdtool to build html docs using rd2
+ * Minor debian/copyright cleanup to get rid of stupid lintian warning about
+ boilerplate
+ * Change Build-Depends to Build-Depends-Indep
+ * Update standards version to 3.6.2. No changes needed.
+ * Add ruby1.8 to recommends for libbio-ruby1.8
+
+ -- David Nusinow <dnusinow at debian.org> Thu, 1 Sep 2005 14:04:35 -0400
+
+bioruby (0.6.2-3) unstable; urgency=low
+
+ * Add watch file
+
+ -- David Nusinow <dnusinow at debian.org> Thu, 7 Apr 2005 22:12:44 -0400
+
+bioruby (0.6.2-2) unstable; urgency=low
+
+ * Depend on libruby1.8 instead of ruby1.8 to bring in line with ruby policy
+ * Add Recommends on blast2 for local blast
+ * Depend on docbook-to-man; closes: #302360
+
+ -- David Nusinow <dnusinow at debian.org> Tue, 1 Feb 2005 00:25:45 -0500
+
+bioruby (0.6.2-1) unstable; urgency=low
+
+ * Initial Release.
+
+ -- David Nusinow <dnusinow at debian.org> Mon, 31 Jan 2005 11:11:55 -0500
+
Added: trunk/packages/bioruby/trunk/debian/compat
===================================================================
--- trunk/packages/bioruby/trunk/debian/compat (rev 0)
+++ trunk/packages/bioruby/trunk/debian/compat 2009-10-04 06:59:28 UTC (rev 4140)
@@ -0,0 +1 @@
+5
Added: trunk/packages/bioruby/trunk/debian/control
===================================================================
--- trunk/packages/bioruby/trunk/debian/control (rev 0)
+++ trunk/packages/bioruby/trunk/debian/control 2009-10-04 06:59:28 UTC (rev 4140)
@@ -0,0 +1,35 @@
+Source: bioruby
+Section: science
+Priority: optional
+Maintainer: David Nusinow <dnusinow at debian.org>
+Build-Depends: debhelper (>= 5.0.0), ruby
+Build-Depends-Indep: docbook-to-man, rdtool
+Standards-Version: 3.7.2.0
+
+Package: libbio-ruby1.8
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}, libruby1.8
+Recommends: blast2, ruby1.8
+Description: bioruby 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 and stupid) to maximize the usability and the
+ efficiency for biologists as a daily tool. The project was started in Japan
+ and supported by University of Tokyo (Human Genome Center), Kyoto University
+ (Bioinformatics Center) and the Open Bio Foundation.
+ .
+ http://www.bioruby.org
+
+Package: libbio-ruby
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}, libbio-ruby1.8
+Description: bioruby 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 and stupid) to maximize the usability and the
+ efficiency for biologists as a daily tool. The project was started in Japan
+ and supported by University of Tokyo (Human Genome Center), Kyoto University
+ (Bioinformatics Center) and the Open Bio Foundation.
+ .
+ This project is a dependency package, which depends on Debian's default Ruby
+ version (currently 1.8.x)
Added: trunk/packages/bioruby/trunk/debian/copyright
===================================================================
--- trunk/packages/bioruby/trunk/debian/copyright (rev 0)
+++ trunk/packages/bioruby/trunk/debian/copyright 2009-10-04 06:59:28 UTC (rev 4140)
@@ -0,0 +1,75 @@
+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'.
+
Added: trunk/packages/bioruby/trunk/debian/docs
===================================================================
--- trunk/packages/bioruby/trunk/debian/docs (rev 0)
+++ trunk/packages/bioruby/trunk/debian/docs 2009-10-04 06:59:28 UTC (rev 4140)
@@ -0,0 +1 @@
+README
Added: trunk/packages/bioruby/trunk/debian/rules
===================================================================
--- trunk/packages/bioruby/trunk/debian/rules (rev 0)
+++ trunk/packages/bioruby/trunk/debian/rules 2009-10-04 06:59:28 UTC (rev 4140)
@@ -0,0 +1,84 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+RUBYVER = 1.8
+RUBYDIR = usr/lib/ruby
+SITELIBDIR = $(RUBYDIR)/$(RUBYVER)
+PREFIXDIR = $(CURDIR)/debian/libbio-ruby$(RUBYVER)
+
+configure: configure-stamp
+configure-stamp:
+ dh_testdir
+ ruby install.rb config --prefix=$(PREFIXDIR)/usr --site-ruby-common=$(PREFIXDIR)/$(RUBYDIR) --site-ruby=$(PREFIXDIR)/$(SITELIBDIR)
+ ruby install.rb setup
+ ruby install.rb test
+ touch configure-stamp
+
+build: build-stamp
+
+build-stamp: configure-stamp
+ dh_testdir
+ # Build manpages
+ docbook-to-man debian/br_biofetch.rb.sgml > br_biofetch.1
+ docbook-to-man debian/br_bioflat.rb.sgml > br_bioflat.1
+ docbook-to-man debian/br_biogetseq.rb.sgml > br_biogetseq.1
+ docbook-to-man debian/br_pmfetch.rb.sgml > br_pmfetch.1
+ touch build-stamp
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp configure-stamp
+ dh_clean
+ ruby install.rb config --prefix=$(CURDIR)/debian/libbio-ruby$(RUBYVER)/usr
+ ruby install.rb clean
+ # Remove generated documents
+ rm -f br_biofetch.1
+ rm -f br_bioflat.1
+ rm -f br_biogetseq.1
+ rm -f br_pmfetch.1
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+
+ ruby install.rb install
+ for FILE in `ls $(PREFIXDIR)/usr/bin/*rb`; do \
+ BINNAME=$$(echo $$FILE | sed 's/\.rb$$//'); \
+ mv $$FILE $$BINNAME; \
+ done
+
+ # Install docs
+ dh_installdocs doc etc/bioinformatics/seqdatabase.ini
+ dh_installexamples sample/*
+
+# Build architecture-independent files here.
+binary-indep: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs ChangeLog
+ dh_installdocs
+ dh_installman br_biofetch.1 br_bioflat.1 br_biogetseq.1 br_pmfetch.1
+ dh_compress
+ dh_fixperms
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+# Build architecture-dependent files here.
+binary-arch: build install
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install configure
Property changes on: trunk/packages/bioruby/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/bioruby/trunk/debian/watch
===================================================================
--- trunk/packages/bioruby/trunk/debian/watch (rev 0)
+++ trunk/packages/bioruby/trunk/debian/watch 2009-10-04 06:59:28 UTC (rev 4140)
@@ -0,0 +1,3 @@
+version=3
+
+http://bioruby.org/archive/bioruby-(.*)\.tar\.gz
Modified: trunk/packages/phylip/trunk/debian/patches/series
===================================================================
--- trunk/packages/phylip/trunk/debian/patches/series 2009-10-03 21:57:59 UTC (rev 4139)
+++ trunk/packages/phylip/trunk/debian/patches/series 2009-10-04 06:59:28 UTC (rev 4140)
@@ -1,3 +1,3 @@
-01_Makefile.patch
-01_src_Makefile.patch
+01_src_Makefile.patch
01_src_phylip_h
+02_fix_treedist
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