[med-svn] r6705 - in trunk/packages/ampliconnoise/trunk/debian: . patches
Timothy Booth
tbooth-guest at alioth.debian.org
Thu Apr 28 15:27:21 UTC 2011
Author: tbooth-guest
Date: 2011-04-28 15:27:09 +0000 (Thu, 28 Apr 2011)
New Revision: 6705
Added:
trunk/packages/ampliconnoise/trunk/debian/ampliconnoise.pod
trunk/packages/ampliconnoise/trunk/debian/get-orig-source
Removed:
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
Modified:
trunk/packages/ampliconnoise/trunk/debian/changelog
trunk/packages/ampliconnoise/trunk/debian/control
trunk/packages/ampliconnoise/trunk/debian/copyright
trunk/packages/ampliconnoise/trunk/debian/patches/fix-path-for-data.patch
trunk/packages/ampliconnoise/trunk/debian/patches/series
trunk/packages/ampliconnoise/trunk/debian/rules
trunk/packages/ampliconnoise/trunk/debian/watch
Log:
Fixed some of the issues pointed out by Andreas and by Lintian.
Added basic manpage.
Added: trunk/packages/ampliconnoise/trunk/debian/ampliconnoise.pod
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/ampliconnoise.pod (rev 0)
+++ trunk/packages/ampliconnoise/trunk/debian/ampliconnoise.pod 2011-04-28 15:27:09 UTC (rev 6705)
@@ -0,0 +1,113 @@
+#!/bin/bash
+echo pod2man -c 'AmpliconNoise Documentation' "$0" ">" `basename "$0" .pod`.1
+exec pod2man -c 'AmpliconNoise Documentation' "$0" > `basename "$0" .pod`.1
+
+=head1 NAME
+
+AmpliconNoise - remove noise from high throughput nucleotide sequence data
+
+=head1 VERSION
+
+This documentation refers to version 1.22
+
+=head1 SYNOPSIS
+
+See B</usr/share/doc/ampliconnoise/Doc.pdf.gz> for details of how to run.
+
+=head1 DESCRIPTION
+
+The following tools are included. Most of them have an MPI equivalent, for example
+SeqNoise has an equivalent SeqNoiseM which can be used with mpirun.
+
+B<FastaUnique> - dereplicates fasta file
+ -in string input file name
+ Options:
+
+B<FCluster>
+ -in string distance input file name
+ -out string output file stub
+ Options:
+ -r resolution
+ -a average linkage
+ -w use weights
+ -i read identifiers
+ -s scale dist.
+
+B<NDist> - pairwise Needleman-Wunsch sequence distance matrix from a fasta file
+ -in string fata file name
+ Options:
+ -i output identifiers
+
+B<Perseus> - slays monsters
+ -sin string seq file name
+ Options:
+ -tin string reference sequence file
+ -a output alignments
+ -d use imbalance
+ -rin string lookup file name
+
+B<PyroDist> - pairwise distance matrix from flowgrams
+ -in string flow file name
+ -out stub out file stub
+ Options:
+ -ni no index in dat file
+ -rin string lookup file name
+
+B<PyroNoise> - clusters flowgrams without alignments
+ -din string flow file name
+ -out string cluster input file name
+ -lin string list file
+ Options:
+ -v verbose
+ -c double initial cut-off
+ -ni no index in dat file
+ -s double precision
+ -rin file lookup file name
+
+B<SeqDist> - pairwise distance matrix from a fasta file
+ -in string fasta file name
+ Options:
+ -i output identifiers
+ -rin string lookup file name
+
+B<SeqNoise> - clusters sequences
+ -in string sequence file name
+ -din string distance matrix file name
+ -out string cluster input file name
+ -lin string list file
+ Options:
+ -min mapping file
+ -v verbose
+ -c double initial cut-off
+ -s double precision
+ -rin string lookup file name
+
+B<SplitClusterEven>
+ -din string dat filename
+ -min string map filename
+ -tin string tree filename
+ -s split size
+ -m min size
+
+=cut
+
+# Here's the line to generate the descriptions above:
+# dpkg -L ampliconnoise | grep ^/usr/bin/ | grep -v 'M$' | sort | bash | sed 's/Can.t find.*/\n/ ; s/^\(.\)/ \1/ ; s/^ -/ -/'
+
+=head1 AUTHOR
+
+All software by Chris Quince (quince at civil.gla.ac.uk)
+This manpage by Tim Booth (tbooth at ceh.ac.uk)
+
+=head1 LICENCE AND COPYRIGHT
+
+Copyright (c) 2009 (quince at civil.gla.ac.uk). All rights reserved.
+
+Released under the Lesser GPL.
+
+Permission is granted for anyone to copy, use, or modify these programs and documents
+for purposes of research or education, provided this copyright notice is retained,
+and note is made of any changes that have been made.
+
+=cut
+
Property changes on: trunk/packages/ampliconnoise/trunk/debian/ampliconnoise.pod
___________________________________________________________________
Added: svn:executable
+ *
Modified: trunk/packages/ampliconnoise/trunk/debian/changelog
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/changelog 2011-04-28 15:17:45 UTC (rev 6704)
+++ trunk/packages/ampliconnoise/trunk/debian/changelog 2011-04-28 15:27:09 UTC (rev 6705)
@@ -1,9 +1,12 @@
-ampliconnoise (1.22-1ubuntu3) lucid; urgency=low
+ampliconnoise (1.22-1ubuntu4) lucid; urgency=low
* Initial upload (Closes: #624362).
[ Tim Booth ]
* Included required data and set paths to find it.
+ * Fixed build dependency on libmpich2-dev
+ * Added a rule to repack the upstream source
+ * Cleanups of boilerplate text in patches and dh files
[ Andreas Tille ]
* debian/control:
@@ -12,7 +15,7 @@
- Standards-Version: 3.9.2 (no changes needed)
- VCS fields
- -- Andreas Tille <tille at debian.org> Thu, 28 Apr 2011 09:03:12 +0200
+ -- Tim Booth <tbooth at ceh.ac.uk> Thu, 28 Apr 2011 11:28:28 +0100
ampliconnoise (1.22-1ubuntu2) lucid; urgency=low
Modified: trunk/packages/ampliconnoise/trunk/debian/control
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/control 2011-04-28 15:17:45 UTC (rev 6704)
+++ trunk/packages/ampliconnoise/trunk/debian/control 2011-04-28 15:27:09 UTC (rev 6705)
@@ -4,7 +4,7 @@
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Tim Booth <tbooth at ceh.ac.uk>, Andreas Tille <tille at debian.org>
-Build-Depends: quilt (>= 0.46-7~), debhelper (>= 7.1~), libgsl0-dev
+Build-Depends: quilt (>= 0.46-7~), debhelper (>= 7.1~), libgsl0-dev, libmpich2-dev (>= 1.2)
Standards-Version: 3.9.2
Homepage: http://code.google.com/p/ampliconnoise/
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/ampliconnoise/trunk/?rev=0&sc=0
@@ -15,10 +15,17 @@
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.
+ AmpliconNoise is a package of applications to clean up high-throughput
+ sequence data. It consists of three main parts:
+ .
+ Pyronoise - does flowgram-based clustering to spot misreads
+ SeqNoise - removes PCR point mutations
+ Perseus - removes PCR chimeras without the need for a set of reference
+ sequences
+ .
+ Previously there was a standalone "Pyronoise" by the same authors and
+ this package includes an updated version. There is also a "Denoiser"
+ in Qiime which is related but distinct.
.
Removing Noise From Pyrosequenced Amplicons
Christopher Quince, Anders Lanzen, Russell J Davenport and Peter J Turnbaugh
Modified: trunk/packages/ampliconnoise/trunk/debian/copyright
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/copyright 2011-04-28 15:17:45 UTC (rev 6704)
+++ trunk/packages/ampliconnoise/trunk/debian/copyright 2011-04-28 15:27:09 UTC (rev 6705)
@@ -10,7 +10,7 @@
Copyright:
- <Copyright (C) 2009-2011 Christopher Quince >
+ Copyright (C) 2009-2011 Christopher Quince
License:
@@ -22,6 +22,3 @@
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/get-orig-source
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/get-orig-source (rev 0)
+++ trunk/packages/ampliconnoise/trunk/debian/get-orig-source 2011-04-28 15:27:09 UTC (rev 6705)
@@ -0,0 +1,21 @@
+#!/bin/sh
+# script to download and repack source package becsue of stray file in top level
+
+set -x
+PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+VERSION=`uscan --verbose --force-download | \
+ grep "Newest version on remote site is .* local version is .*" | \
+ head -n 1 | \
+ sed "s/Newest version on remote site is \([-0-9.]\+\),.*/\1/"`
+
+UPSTREAMNAME=AmpliconNoise
+
+mkdir -p ../tarballs
+cd ../tarballs
+test `ls|wc -l` = 0 || { echo "../tarballs not empty" ; exit 1 ; }
+
+tar -xzf ../${UPSTREAMNAME}V${VERSION}.tar.gz
+rm -f .*
+
+GZIP="--best --no-name" tar -czf "$PKG"_"$VERSION".orig.tar.gz *
+rm -rf *
Deleted: trunk/packages/ampliconnoise/trunk/debian/manpage.1.ex
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/manpage.1.ex 2011-04-28 15:17:45 UTC (rev 6704)
+++ trunk/packages/ampliconnoise/trunk/debian/manpage.1.ex 2011-04-28 15:27:09 UTC (rev 6705)
@@ -1,59 +0,0 @@
-.\" 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).
Deleted: trunk/packages/ampliconnoise/trunk/debian/manpage.sgml.ex
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/manpage.sgml.ex 2011-04-28 15:17:45 UTC (rev 6704)
+++ trunk/packages/ampliconnoise/trunk/debian/manpage.sgml.ex 2011-04-28 15:27:09 UTC (rev 6705)
@@ -1,154 +0,0 @@
-<!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:
--->
Deleted: trunk/packages/ampliconnoise/trunk/debian/manpage.xml.ex
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/manpage.xml.ex 2011-04-28 15:17:45 UTC (rev 6704)
+++ trunk/packages/ampliconnoise/trunk/debian/manpage.xml.ex 2011-04-28 15:27:09 UTC (rev 6705)
@@ -1,291 +0,0 @@
-<?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>
-
Deleted: trunk/packages/ampliconnoise/trunk/debian/menu.ex
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/menu.ex 2011-04-28 15:17:45 UTC (rev 6704)
+++ trunk/packages/ampliconnoise/trunk/debian/menu.ex 2011-04-28 15:27:09 UTC (rev 6705)
@@ -1,2 +0,0 @@
-?package(ampliconnoise):needs="X11|text|vc|wm" section="Applications/see-menu-manual"\
- title="ampliconnoise" command="/usr/bin/ampliconnoise"
Modified: trunk/packages/ampliconnoise/trunk/debian/patches/fix-path-for-data.patch
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/patches/fix-path-for-data.patch 2011-04-28 15:17:45 UTC (rev 6704)
+++ trunk/packages/ampliconnoise/trunk/debian/patches/fix-path-for-data.patch 2011-04-28 15:27:09 UTC (rev 6705)
@@ -1,30 +1,17 @@
-Description: Upstream changes introduced in version 1.22-1ubuntu3
- This patch has been created by dpkg-source during the package build.
- Here's the last changelog entry, hopefully it gives details on why
- those changes were made:
- .
- ampliconnoise (1.22-1ubuntu3) lucid; urgency=low
- .
- * Included required data and set paths to find it.
- .
- The person named in the Author field signed this changelog entry.
Author: Tim Booth <tbooth at ceh.ac.uk>
+Origin: Specific to package
+Bug: None
+Last-Update: 2011-04-28
----
-The information above should follow the Patch Tagging Guidelines, please
-checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
-are templates for supplementary fields that you might want to add:
+The upstream software is built so as to run from the build environment and look for
+data in ../Data. In Debian the binaries belong in /usr/bin and the data belongs
+in /usr/share. With this patch the binaries will run from any directory.
+A better fix would be to allow setting of the Data directory via an environment variable
+or a variable passed to MAKE at build time. This could be contributed back to upstream.
-Origin: <vendor|upstream|other>, <url of original patch>
-Bug: <url in upstream bugtracker>
-Bug-Debian: http://bugs.debian.org/<bugnumber>
-Forwarded: <no|not-needed|url proving that it has been forwarded>
-Reviewed-By: <name and email of someone who approved the patch>
-Last-Update: <YYYY-MM-DD>
-
---- ampliconnoise-1.22.orig/SeqNoise/SeqNoise.h
-+++ ampliconnoise-1.22/SeqNoise/SeqNoise.h
-@@ -113,7 +113,7 @@ typedef struct s_Master
+--- a/SeqNoise/SeqNoise.h
++++ b/SeqNoise/SeqNoise.h
+@@ -113,7 +113,7 @@
/********DEFAULTS***********/
#define DEF_SIGMA 30.0
#define DEF_CUT 0.08
@@ -33,9 +20,9 @@
/***************************/
/******Programming Constants************/
---- ampliconnoise-1.22.orig/SeqDistM/SeqDistM.h
-+++ ampliconnoise-1.22/SeqDistM/SeqDistM.h
-@@ -71,7 +71,7 @@ typedef struct s_Data
+--- a/SeqDistM/SeqDistM.h
++++ b/SeqDistM/SeqDistM.h
+@@ -71,7 +71,7 @@
/* User defined structures */
@@ -44,9 +31,9 @@
typedef struct s_Align
---- ampliconnoise-1.22.orig/SeqDist/SeqDist.h
-+++ ampliconnoise-1.22/SeqDist/SeqDist.h
-@@ -71,7 +71,7 @@ typedef struct s_Data
+--- a/SeqDist/SeqDist.h
++++ b/SeqDist/SeqDist.h
+@@ -71,7 +71,7 @@
/* User defined structures */
@@ -55,9 +42,9 @@
typedef struct s_Align
---- ampliconnoise-1.22.orig/SeqNoiseM/SeqNoiseM.h
-+++ ampliconnoise-1.22/SeqNoiseM/SeqNoiseM.h
-@@ -113,7 +113,7 @@ typedef struct s_Master
+--- a/SeqNoiseM/SeqNoiseM.h
++++ b/SeqNoiseM/SeqNoiseM.h
+@@ -113,7 +113,7 @@
/********DEFAULTS***********/
#define DEF_SIGMA 30.0
#define DEF_CUT 0.08
@@ -66,8 +53,8 @@
/***************************/
/******Programming Constants************/
---- ampliconnoise-1.22.orig/PyroNoiseM/PyroNoiseM.h
-+++ ampliconnoise-1.22/PyroNoiseM/PyroNoiseM.h
+--- a/PyroNoiseM/PyroNoiseM.h
++++ b/PyroNoiseM/PyroNoiseM.h
@@ -36,7 +36,7 @@
#define OVERCALL_THRESH 6.0 /*?*/
@@ -77,8 +64,8 @@
#define OUT_FILE_STUB "-out"
#define INIT_FILE "-lin"
---- ampliconnoise-1.22.orig/PyroNoise/PyroNoise.h
-+++ ampliconnoise-1.22/PyroNoise/PyroNoise.h
+--- a/PyroNoise/PyroNoise.h
++++ b/PyroNoise/PyroNoise.h
@@ -37,7 +37,7 @@
#define OVERCALL_THRESH 6.0 /*?*/
@@ -88,9 +75,9 @@
#define OUT_FILE_STUB "-out"
#define INIT_FILE "-lin"
---- ampliconnoise-1.22.orig/Perseus/Perseus.h
-+++ ampliconnoise-1.22/Perseus/Perseus.h
-@@ -86,7 +86,7 @@ typedef struct s_Data
+--- a/Perseus/Perseus.h
++++ b/Perseus/Perseus.h
+@@ -86,7 +86,7 @@
#define WEIGHTDELIM '_'
#define N_BASES 4
@@ -99,8 +86,8 @@
#ifndef min
#define min(x, y) ((x) < (y) ? (x) : (y))
---- ampliconnoise-1.22.orig/PyroDist/PyroDist.h
-+++ ampliconnoise-1.22/PyroDist/PyroDist.h
+--- a/PyroDist/PyroDist.h
++++ b/PyroDist/PyroDist.h
@@ -34,7 +34,7 @@
#define LEFT 1
#define UP 2
Modified: trunk/packages/ampliconnoise/trunk/debian/patches/series
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/patches/series 2011-04-28 15:17:45 UTC (rev 6704)
+++ trunk/packages/ampliconnoise/trunk/debian/patches/series 2011-04-28 15:27:09 UTC (rev 6705)
@@ -1,2 +1 @@
-fix-clean-of-seqnoisem.patch
fix-path-for-data.patch
Modified: trunk/packages/ampliconnoise/trunk/debian/rules
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/rules 2011-04-28 15:17:45 UTC (rev 6704)
+++ trunk/packages/ampliconnoise/trunk/debian/rules 2011-04-28 15:27:09 UTC (rev 6705)
@@ -1,11 +1,6 @@
#!/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
@@ -17,3 +12,19 @@
dh_install bin/* /usr/bin
dh_install Data/* /usr/share/ampliconnoise/Data/
+#A typo in the upstream Makefile prevents proper cleaning.
+override_dh_clean:
+ dh_clean
+ rm -f *.o SeqNoiseM/SeqNoiseM
+ rm -f manpage_all.1
+
+override_dh_installman:
+ debian/ampliconnoise.pod
+ dh_installman ampliconnoise.1
+ ( for f in bin/* ; do \
+ ln -s ampliconnoise.1 debian/ampliconnoise/usr/share/man/man1/`basename "$$f"`.1 ; \
+ done )
+
+get-orig-source:
+ . debian/get-orig-source
+
Modified: trunk/packages/ampliconnoise/trunk/debian/watch
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/watch 2011-04-28 15:17:45 UTC (rev 6704)
+++ trunk/packages/ampliconnoise/trunk/debian/watch 2011-04-28 15:27:09 UTC (rev 6705)
@@ -1,8 +1,3 @@
-# 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
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