[med-svn] r6679 - in trunk/packages: . ampliconnoise ampliconnoise/trunk ampliconnoise/trunk/debian ampliconnoise/trunk/debian/patches
Timothy Booth
tbooth-guest at alioth.debian.org
Wed Apr 27 15:52:25 UTC 2011
Author: tbooth-guest
Date: 2011-04-27 15:52:10 +0000 (Wed, 27 Apr 2011)
New Revision: 6679
Added:
trunk/packages/ampliconnoise/
trunk/packages/ampliconnoise/trunk/
trunk/packages/ampliconnoise/trunk/debian/
trunk/packages/ampliconnoise/trunk/debian/README.Debian
trunk/packages/ampliconnoise/trunk/debian/README.source
trunk/packages/ampliconnoise/trunk/debian/ampliconnoise.doc-base.EX
trunk/packages/ampliconnoise/trunk/debian/ampliconnoise.docs
trunk/packages/ampliconnoise/trunk/debian/changelog
trunk/packages/ampliconnoise/trunk/debian/compat
trunk/packages/ampliconnoise/trunk/debian/control
trunk/packages/ampliconnoise/trunk/debian/copyright
trunk/packages/ampliconnoise/trunk/debian/docs
trunk/packages/ampliconnoise/trunk/debian/manpage.1.ex
trunk/packages/ampliconnoise/trunk/debian/manpage.sgml.ex
trunk/packages/ampliconnoise/trunk/debian/manpage.xml.ex
trunk/packages/ampliconnoise/trunk/debian/menu.ex
trunk/packages/ampliconnoise/trunk/debian/patches/
trunk/packages/ampliconnoise/trunk/debian/patches/install_to_destdir.patch
trunk/packages/ampliconnoise/trunk/debian/patches/remove-unneeded-linking.patch
trunk/packages/ampliconnoise/trunk/debian/patches/series
trunk/packages/ampliconnoise/trunk/debian/rules
trunk/packages/ampliconnoise/trunk/debian/watch
Log:
First bash at AmpliconNoise package. Fairly simple. Probably wants a single manpage for all
command line apps referencing the main doc.
Added: trunk/packages/ampliconnoise/trunk/debian/README.Debian
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/ampliconnoise/trunk/debian/README.Debian 2011-04-27 15:52:10 UTC (rev 6679)
@@ -0,0 +1,7 @@
+ampliconnoise for Debian
+------------------------
+
+See Doc.pdf for guidance on running this application. Note that AmpliconNoise requires
+flowgrams in text form to operate on. If you only have the SFF files available then one
+way to export in text-based format is to use Qiime version 1.2.1 or newer and run the
+process_sff script with the -f flag.
Added: trunk/packages/ampliconnoise/trunk/debian/README.source
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/README.source (rev 0)
+++ trunk/packages/ampliconnoise/trunk/debian/README.source 2011-04-27 15:52:10 UTC (rev 6679)
@@ -0,0 +1,17 @@
+ampliconnoise for Debian
+------------------------
+
+<this file describes information about the source package, see Debian policy
+manual section 4.14. You WILL either need to modify or delete this file>
+
+This package uses quilt to manage all modifications to the upstream
+source. Changes are stored in the source package as diffs in
+debian/patches and applied during the build. Please see:
+
+ /usr/share/doc/quilt/README.source
+
+for more information on how to apply the patches, modify patches, or
+remove a patch.
+
+
+
Added: trunk/packages/ampliconnoise/trunk/debian/ampliconnoise.doc-base.EX
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/ampliconnoise.doc-base.EX (rev 0)
+++ trunk/packages/ampliconnoise/trunk/debian/ampliconnoise.doc-base.EX 2011-04-27 15:52:10 UTC (rev 6679)
@@ -0,0 +1,20 @@
+Document: ampliconnoise
+Title: Debian ampliconnoise Manual
+Author: <insert document author here>
+Abstract: This manual describes what ampliconnoise is
+ and how it can be used to
+ manage online manuals on Debian systems.
+Section: unknown
+
+Format: debiandoc-sgml
+Files: /usr/share/doc/ampliconnoise/ampliconnoise.sgml.gz
+
+Format: postscript
+Files: /usr/share/doc/ampliconnoise/ampliconnoise.ps.gz
+
+Format: text
+Files: /usr/share/doc/ampliconnoise/ampliconnoise.text.gz
+
+Format: HTML
+Index: /usr/share/doc/ampliconnoise/html/index.html
+Files: /usr/share/doc/ampliconnoise/html/*.html
Added: trunk/packages/ampliconnoise/trunk/debian/ampliconnoise.docs
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/ampliconnoise.docs (rev 0)
+++ trunk/packages/ampliconnoise/trunk/debian/ampliconnoise.docs 2011-04-27 15:52:10 UTC (rev 6679)
@@ -0,0 +1 @@
+Doc.pdf
Added: trunk/packages/ampliconnoise/trunk/debian/changelog
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/changelog (rev 0)
+++ trunk/packages/ampliconnoise/trunk/debian/changelog 2011-04-27 15:52:10 UTC (rev 6679)
@@ -0,0 +1,11 @@
+ampliconnoise (1.22-1ubuntu1) lucid; urgency=low
+
+ * Build for Lucid.
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Wed, 27 Apr 2011 16:09:27 +0100
+
+ampliconnoise (1.22-1) unstable; urgency=low
+
+ * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Wed, 27 Apr 2011 14:48:11 +0100
Added: trunk/packages/ampliconnoise/trunk/debian/compat
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/compat (rev 0)
+++ trunk/packages/ampliconnoise/trunk/debian/compat 2011-04-27 15:52:10 UTC (rev 6679)
@@ -0,0 +1 @@
+7
Added: trunk/packages/ampliconnoise/trunk/debian/control
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/control (rev 0)
+++ trunk/packages/ampliconnoise/trunk/debian/control 2011-04-27 15:52:10 UTC (rev 6679)
@@ -0,0 +1,21 @@
+Source: ampliconnoise
+Section: science
+Priority: extra
+Maintainer: Tim Booth <tbooth at ceh.ac.uk>
+Build-Depends: quilt (>= 0.46-7~), debhelper (>= 7), libgsl0-dev
+Standards-Version: 3.8.3
+Homepage: http://code.google.com/p/ampliconnoise/
+
+Package: ampliconnoise
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, libgsl0ldbl, mafft
+Recommends: mpi-default-bin
+Description: Programs for the removal of noise from 454 sequenced PCR amplicons
+ AmpliconNoise is a collection of programs for the removal of noise from 454
+ sequenced PCR amplicons. It involves two denoising steps, the removal of noise
+ from the sequencing itself and the removal of PCR point errors.
+ This project also includes the Perseus algorithm for chimera removal.
+ .
+ Removing Noise From Pyrosequenced Amplicons
+ Christopher Quince, Anders Lanzen, Russell J Davenport and Peter J Turnbaugh
+ BMC Bioinformatics 2011, 12:38doi:10.1186/1471-2105-12-38
Added: trunk/packages/ampliconnoise/trunk/debian/copyright
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/copyright (rev 0)
+++ trunk/packages/ampliconnoise/trunk/debian/copyright 2011-04-27 15:52:10 UTC (rev 6679)
@@ -0,0 +1,27 @@
+This work was packaged for Debian by:
+
+ Tim Booth <tbooth at ceh.ac.uk> on Wed, 27 Apr 2011 14:48:11 +0100
+
+It was downloaded from http://code.google.com/p/ampliconnoise/
+
+Upstream Author(s):
+
+ Chris Quince <quince at civil.gla.ac.uk>
+
+Copyright:
+
+ <Copyright (C) 2009-2011 Christopher Quince >
+
+License:
+
+ GNU Lesser GPL
+
+The Debian packaging is:
+
+ Copyright (C) 2011 Tim Booth <tbooth at ceh.ac.uk>
+
+and is licensed under the GPL version 3,
+see `/usr/share/common-licenses/GPL-3'.
+
+# Please also look if there are files or directories which have a
+# different copyright/license attached and list them here.
Added: trunk/packages/ampliconnoise/trunk/debian/manpage.1.ex
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/manpage.1.ex (rev 0)
+++ trunk/packages/ampliconnoise/trunk/debian/manpage.1.ex 2011-04-27 15:52:10 UTC (rev 6679)
@@ -0,0 +1,59 @@
+.\" Hey, EMACS: -*- nroff -*-
+.\" First parameter, NAME, should be all caps
+.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
+.\" other parameters are allowed: see man(7), man(1)
+.TH AMPLICONNOISE SECTION "April 27, 2011"
+.\" Please adjust this date whenever revising the manpage.
+.\"
+.\" Some roff macros, for reference:
+.\" .nh disable hyphenation
+.\" .hy enable hyphenation
+.\" .ad l left justify
+.\" .ad b justify to both left and right margins
+.\" .nf disable filling
+.\" .fi enable filling
+.\" .br insert line break
+.\" .sp <n> insert n+1 empty lines
+.\" for manpage-specific macros, see man(7)
+.SH NAME
+ampliconnoise \- program to do something
+.SH SYNOPSIS
+.B ampliconnoise
+.RI [ options ] " files" ...
+.br
+.B bar
+.RI [ options ] " files" ...
+.SH DESCRIPTION
+This manual page documents briefly the
+.B ampliconnoise
+and
+.B bar
+commands.
+.PP
+.\" TeX users may be more comfortable with the \fB<whatever>\fP and
+.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
+.\" respectively.
+\fBampliconnoise\fP is a program that...
+.SH OPTIONS
+These programs follow the usual GNU command line syntax, with long
+options starting with two dashes (`-').
+A summary of options is included below.
+For a complete description, see the Info files.
+.TP
+.B \-h, \-\-help
+Show summary of options.
+.TP
+.B \-v, \-\-version
+Show version of program.
+.SH SEE ALSO
+.BR bar (1),
+.BR baz (1).
+.br
+The programs are documented fully by
+.IR "The Rise and Fall of a Fooish Bar" ,
+available via the Info system.
+.SH AUTHOR
+ampliconnoise was written by <upstream author>.
+.PP
+This manual page was written by Tim Booth <tbooth at ceh.ac.uk>,
+for the Debian project (and may be used by others).
Added: trunk/packages/ampliconnoise/trunk/debian/manpage.sgml.ex
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/manpage.sgml.ex (rev 0)
+++ trunk/packages/ampliconnoise/trunk/debian/manpage.sgml.ex 2011-04-27 15:52:10 UTC (rev 6679)
@@ -0,0 +1,154 @@
+<!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>FIRSTNAME</firstname>">
+ <!ENTITY dhsurname "<surname>SURNAME</surname>">
+ <!-- Please adjust the date whenever revising the manpage. -->
+ <!ENTITY dhdate "<date>April 27, 2011</date>">
+ <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+ allowed: see man(7), man(1). -->
+ <!ENTITY dhsection "<manvolnum>SECTION</manvolnum>">
+ <!ENTITY dhemail "<email>tbooth at ceh.ac.uk</email>">
+ <!ENTITY dhusername "Tim Booth">
+ <!ENTITY dhucpackage "<refentrytitle>AMPLICONNOISE</refentrytitle>">
+ <!ENTITY dhpackage "ampliconnoise">
+
+ <!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>2003</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ &dhdate;
+ </refentryinfo>
+ <refmeta>
+ &dhucpackage;
+
+ &dhsection;
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+
+ <refpurpose>program to do something</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+
+ <arg><option>-e <replaceable>this</replaceable></option></arg>
+
+ <arg><option>--example <replaceable>that</replaceable></option></arg>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1>
+ <title>DESCRIPTION</title>
+
+ <para>This manual page documents briefly the
+ <command>&dhpackage;</command> and <command>bar</command>
+ commands.</para>
+
+ <para>This manual page was written for the &debian; distribution
+ because the original program does not have a manual page.
+ Instead, it has documentation in the &gnu;
+ <application>Info</application> format; see below.</para>
+
+ <para><command>&dhpackage;</command> is a program that...</para>
+
+ </refsect1>
+ <refsect1>
+ <title>OPTIONS</title>
+
+ <para>These programs follow the usual &gnu; command line syntax,
+ with long options starting with two dashes (`-'). A summary of
+ options is included below. For a complete description, see the
+ <application>Info</application> files.</para>
+
+ <variablelist>
+ <varlistentry>
+ <term><option>-h</option>
+ <option>--help</option>
+ </term>
+ <listitem>
+ <para>Show summary of options.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-v</option>
+ <option>--version</option>
+ </term>
+ <listitem>
+ <para>Show version of program.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+ <refsect1>
+ <title>SEE ALSO</title>
+
+ <para>bar (1), baz (1).</para>
+
+ <para>The programs are documented fully by <citetitle>The Rise and
+ Fall of a Fooish Bar</citetitle> available via the
+ <application>Info</application> system.</para>
+ </refsect1>
+ <refsect1>
+ <title>AUTHOR</title>
+
+ <para>This manual page was written by &dhusername; &dhemail; for
+ the &debian; system (and 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/ampliconnoise/trunk/debian/manpage.xml.ex
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/manpage.xml.ex (rev 0)
+++ trunk/packages/ampliconnoise/trunk/debian/manpage.xml.ex 2011-04-27 15:52:10 UTC (rev 6679)
@@ -0,0 +1,291 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.5//EN"
+"http://www.oasis-open.org/docbook/xml/4.5/docbookx.dtd" [
+
+<!--
+
+`xsltproc -''-nonet \
+ -''-param man.charmap.use.subset "0" \
+ -''-param make.year.ranges "1" \
+ -''-param make.single.year.ranges "1" \
+ /usr/share/xml/docbook/stylesheet/nwalsh/manpages/docbook.xsl \
+ manpage.xml'
+
+A manual page <package>.<section> will be generated. You may view the
+manual page with: nroff -man <package>.<section> | less'. A typical entry
+in a Makefile or Makefile.am is:
+
+DB2MAN = /usr/share/sgml/docbook/stylesheet/xsl/nwalsh/manpages/docbook.xsl
+XP = xsltproc -''-nonet -''-param man.charmap.use.subset "0"
+
+manpage.1: manpage.xml
+ $(XP) $(DB2MAN) $<
+
+The xsltproc binary is found in the xsltproc package. The XSL files are in
+docbook-xsl. A description of the parameters you can use can be found in the
+docbook-xsl-doc-* packages. 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 xsltproc and docbook-xsl in your Build-Depends control field.
+Alternatively use the xmlto command/package. That will also automatically
+pull in xsltproc and docbook-xsl.
+
+Notes for using docbook2x: docbook2x-man does not automatically create the
+AUTHOR(S) and COPYRIGHT sections. In this case, please add them manually as
+<refsect1> ... </refsect1>.
+
+To disable the automatic creation of the AUTHOR(S) and COPYRIGHT sections
+read /usr/share/doc/docbook-xsl/doc/manpages/authors.html. This file can be
+found in the docbook-xsl-doc-html package.
+
+Validation can be done using: `xmllint -''-noout -''-valid manpage.xml`
+
+General documentation about man-pages and man-page-formatting:
+man(1), man(7), http://www.tldp.org/HOWTO/Man-Page/
+
+-->
+
+ <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+ <!ENTITY dhfirstname "FIRSTNAME">
+ <!ENTITY dhsurname "SURNAME">
+ <!-- dhusername could also be set to "&dhfirstname; &dhsurname;". -->
+ <!ENTITY dhusername "Tim Booth">
+ <!ENTITY dhemail "tbooth at ceh.ac.uk">
+ <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+ allowed: see man(7), man(1) and
+ http://www.tldp.org/HOWTO/Man-Page/q2.html. -->
+ <!ENTITY dhsection "SECTION">
+ <!-- TITLE should be something like "User commands" or similar (see
+ http://www.tldp.org/HOWTO/Man-Page/q2.html). -->
+ <!ENTITY dhtitle "ampliconnoise User Manual">
+ <!ENTITY dhucpackage "AMPLICONNOISE">
+ <!ENTITY dhpackage "ampliconnoise">
+]>
+
+<refentry>
+ <refentryinfo>
+ <title>&dhtitle;</title>
+ <productname>&dhpackage;</productname>
+ <authorgroup>
+ <author>
+ <firstname>&dhfirstname;</firstname>
+ <surname>&dhsurname;</surname>
+ <contrib>Wrote this manpage for the Debian system.</contrib>
+ <address>
+ <email>&dhemail;</email>
+ </address>
+ </author>
+ </authorgroup>
+ <copyright>
+ <year>2007</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ <legalnotice>
+ <para>This manual page was written for the Debian system
+ (and may be used by others).</para>
+ <para>Permission is granted to copy, distribute and/or modify this
+ document under the terms of the GNU General Public License,
+ Version 2 or (at your option) 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
+ <filename>/usr/share/common-licenses/GPL</filename>.</para>
+ </legalnotice>
+ </refentryinfo>
+ <refmeta>
+ <refentrytitle>&dhucpackage;</refentrytitle>
+ <manvolnum>&dhsection;</manvolnum>
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+ <refpurpose>program to do something</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <!-- These are several examples, how syntaxes could look -->
+ <arg choice="plain"><option>-e <replaceable>this</replaceable></option></arg>
+ <arg choice="opt"><option>--example=<parameter>that</parameter></option></arg>
+ <arg choice="opt">
+ <group choice="req">
+ <arg choice="plain"><option>-e</option></arg>
+ <arg choice="plain"><option>--example</option></arg>
+ </group>
+ <replaceable class="option">this</replaceable>
+ </arg>
+ <arg choice="opt">
+ <group choice="req">
+ <arg choice="plain"><option>-e</option></arg>
+ <arg choice="plain"><option>--example</option></arg>
+ </group>
+ <group choice="req">
+ <arg choice="plain"><replaceable>this</replaceable></arg>
+ <arg choice="plain"><replaceable>that</replaceable></arg>
+ </group>
+ </arg>
+ </cmdsynopsis>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <!-- Normally the help and version options make the programs stop
+ right after outputting the requested information. -->
+ <group choice="opt">
+ <arg choice="plain">
+ <group choice="req">
+ <arg choice="plain"><option>-h</option></arg>
+ <arg choice="plain"><option>--help</option></arg>
+ </group>
+ </arg>
+ <arg choice="plain">
+ <group choice="req">
+ <arg choice="plain"><option>-v</option></arg>
+ <arg choice="plain"><option>--version</option></arg>
+ </group>
+ </arg>
+ </group>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1 id="description">
+ <title>DESCRIPTION</title>
+ <para>This manual page documents briefly the
+ <command>&dhpackage;</command> and <command>bar</command>
+ commands.</para>
+ <para>This manual page was written for the Debian distribution
+ because the original program does not have a manual page.
+ Instead, it has documentation in the GNU <citerefentry>
+ <refentrytitle>info</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry> format; see below.</para>
+ <para><command>&dhpackage;</command> is a program that...</para>
+ </refsect1>
+ <refsect1 id="options">
+ <title>OPTIONS</title>
+ <para>The program follows the usual GNU command line syntax,
+ with long options starting with two dashes (`-'). A summary of
+ options is included below. For a complete description, see the
+ <citerefentry>
+ <refentrytitle>info</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry> files.</para>
+ <variablelist>
+ <!-- Use the variablelist.term.separator and the
+ variablelist.term.break.after parameters to
+ control the term elements. -->
+ <varlistentry>
+ <term><option>-e <replaceable>this</replaceable></option></term>
+ <term><option>--example=<replaceable>that</replaceable></option></term>
+ <listitem>
+ <para>Does this and that.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-h</option></term>
+ <term><option>--help</option></term>
+ <listitem>
+ <para>Show summary of options.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-v</option></term>
+ <term><option>--version</option></term>
+ <listitem>
+ <para>Show version of program.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+ <refsect1 id="files">
+ <title>FILES</title>
+ <variablelist>
+ <varlistentry>
+ <term><filename>/etc/foo.conf</filename></term>
+ <listitem>
+ <para>The system-wide configuration file to control the
+ behaviour of <application>&dhpackage;</application>. See
+ <citerefentry>
+ <refentrytitle>foo.conf</refentrytitle>
+ <manvolnum>5</manvolnum>
+ </citerefentry> for further details.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><filename>${HOME}/.foo.conf</filename></term>
+ <listitem>
+ <para>The per-user configuration file to control the
+ behaviour of <application>&dhpackage;</application>. See
+ <citerefentry>
+ <refentrytitle>foo.conf</refentrytitle>
+ <manvolnum>5</manvolnum>
+ </citerefentry> for further details.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+ <refsect1 id="environment">
+ <title>ENVIONMENT</title>
+ <variablelist>
+ <varlistentry>
+ <term><envar>FOO_CONF</envar></term>
+ <listitem>
+ <para>If used, the defined file is used as configuration
+ file (see also <xref linkend="files"/>).</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+ <refsect1 id="diagnostics">
+ <title>DIAGNOSTICS</title>
+ <para>The following diagnostics may be issued
+ on <filename class="devicefile">stderr</filename>:</para>
+ <variablelist>
+ <varlistentry>
+ <term><errortext>Bad configuration file. Exiting.</errortext></term>
+ <listitem>
+ <para>The configuration file seems to contain a broken configuration
+ line. Use the <option>--verbose</option> option, to get more info.
+ </para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ <para><command>&dhpackage;</command> provides some return codes, that can
+ be used in scripts:</para>
+ <segmentedlist>
+ <segtitle>Code</segtitle>
+ <segtitle>Diagnostic</segtitle>
+ <seglistitem>
+ <seg><errorcode>0</errorcode></seg>
+ <seg>Program exited successfully.</seg>
+ </seglistitem>
+ <seglistitem>
+ <seg><errorcode>1</errorcode></seg>
+ <seg>The configuration file seems to be broken.</seg>
+ </seglistitem>
+ </segmentedlist>
+ </refsect1>
+ <refsect1 id="bugs">
+ <!-- Or use this section to tell about upstream BTS. -->
+ <title>BUGS</title>
+ <para>The program is currently limited to only work
+ with the <package>foobar</package> library.</para>
+ <para>The upstreams <acronym>BTS</acronym> can be found
+ at <ulink url="http://bugzilla.foo.tld"/>.</para>
+ </refsect1>
+ <refsect1 id="see_also">
+ <title>SEE ALSO</title>
+ <!-- In alpabetical order. -->
+ <para><citerefentry>
+ <refentrytitle>bar</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>, <citerefentry>
+ <refentrytitle>baz</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>, <citerefentry>
+ <refentrytitle>foo.conf</refentrytitle>
+ <manvolnum>5</manvolnum>
+ </citerefentry></para>
+ <para>The programs are documented fully by <citetitle>The Rise and
+ Fall of a Fooish Bar</citetitle> available via the <citerefentry>
+ <refentrytitle>info</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry> system.</para>
+ </refsect1>
+</refentry>
+
Added: trunk/packages/ampliconnoise/trunk/debian/menu.ex
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/menu.ex (rev 0)
+++ trunk/packages/ampliconnoise/trunk/debian/menu.ex 2011-04-27 15:52:10 UTC (rev 6679)
@@ -0,0 +1,2 @@
+?package(ampliconnoise):needs="X11|text|vc|wm" section="Applications/see-menu-manual"\
+ title="ampliconnoise" command="/usr/bin/ampliconnoise"
Added: trunk/packages/ampliconnoise/trunk/debian/patches/install_to_destdir.patch
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/patches/install_to_destdir.patch (rev 0)
+++ trunk/packages/ampliconnoise/trunk/debian/patches/install_to_destdir.patch 2011-04-27 15:52:10 UTC (rev 6679)
@@ -0,0 +1,9 @@
+--- a/makefile
++++ b/makefile
+@@ -42,4 +42,5 @@
+ cp SeqNoiseM/SeqNoiseM bin
+ cp SplitClusterEven/SplitClusterEven bin
+ cp Perseus/Perseus bin
+-
++ #Added for Deb package
++ mv bin/* $(DESTDIR)/usr/bin
Added: trunk/packages/ampliconnoise/trunk/debian/patches/remove-unneeded-linking.patch
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/patches/remove-unneeded-linking.patch (rev 0)
+++ trunk/packages/ampliconnoise/trunk/debian/patches/remove-unneeded-linking.patch 2011-04-27 15:52:10 UTC (rev 6679)
@@ -0,0 +1,11 @@
+--- a/Perseus/makefile
++++ b/Perseus/makefile
+@@ -2,7 +2,7 @@
+ CFLAGS = -O3
+ EFLAGS =
+ EFILE = Perseus
+-LIBS = -lm -lgsl -lgslcblas
++LIBS = -lm -lgsl # -lgslcblas
+ OBJS = Perseus.o
+
+ $(EFILE) : $(OBJS)
Added: trunk/packages/ampliconnoise/trunk/debian/rules
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/rules (rev 0)
+++ trunk/packages/ampliconnoise/trunk/debian/rules 2011-04-27 15:52:10 UTC (rev 6679)
@@ -0,0 +1,18 @@
+#!/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
+
+%:
+ dh --with quilt $@
+
+override_dh_auto_install:
+ make install
+ dh_install bin/* /usr/bin
+
Property changes on: trunk/packages/ampliconnoise/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/ampliconnoise/trunk/debian/watch
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/watch (rev 0)
+++ trunk/packages/ampliconnoise/trunk/debian/watch 2011-04-27 15:52:10 UTC (rev 6679)
@@ -0,0 +1,12 @@
+# Example watch control file for uscan
+# Rename this file to "watch" and then you can run the "uscan" command
+# to check for upstream updates and more.
+# See uscan(1) for format
+
+# Compulsory line, this is a version 3 file
+version=3
+
+# Uncomment to examine a Webpage
+# <Webpage URL> <string match>
+http://code.google.com/p/ampliconnoise/downloads/list .*AmpliconNoiseV([.0-9]*)\.tar\.gz
+
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