[med-svn] r5421 - in trunk/packages: . autodock-vina autodock-vina/trunk autodock-vina/trunk/debian autodock-vina/trunk/debian/patches autodock-vina/trunk/debian/source
yask gupta
yask-guest at alioth.debian.org
Thu Nov 11 15:40:30 UTC 2010
Author: yask-guest
Date: 2010-11-11 15:40:24 +0000 (Thu, 11 Nov 2010)
New Revision: 5421
Added:
trunk/packages/autodock-vina/
trunk/packages/autodock-vina/trunk/
trunk/packages/autodock-vina/trunk/debian/
trunk/packages/autodock-vina/trunk/debian/README.Debian
trunk/packages/autodock-vina/trunk/debian/README.source
trunk/packages/autodock-vina/trunk/debian/autodock-vina.doc-base.EX
trunk/packages/autodock-vina/trunk/debian/autodock-vina.install
trunk/packages/autodock-vina/trunk/debian/changelog
trunk/packages/autodock-vina/trunk/debian/compat
trunk/packages/autodock-vina/trunk/debian/control
trunk/packages/autodock-vina/trunk/debian/copyright
trunk/packages/autodock-vina/trunk/debian/docs
trunk/packages/autodock-vina/trunk/debian/manpage.1.ex
trunk/packages/autodock-vina/trunk/debian/manpage.sgml.ex
trunk/packages/autodock-vina/trunk/debian/manpage.xml.ex
trunk/packages/autodock-vina/trunk/debian/patches/
trunk/packages/autodock-vina/trunk/debian/patches/debian-changes-1.1.1-1
trunk/packages/autodock-vina/trunk/debian/patches/series
trunk/packages/autodock-vina/trunk/debian/patches/top_level_Makefile.patch
trunk/packages/autodock-vina/trunk/debian/rules
trunk/packages/autodock-vina/trunk/debian/source/
trunk/packages/autodock-vina/trunk/debian/source/format
trunk/packages/autodock-vina/trunk/debian/watch
Log:
Preparing for upload of new autodock-vina package for experimental.
Added: trunk/packages/autodock-vina/trunk/debian/README.Debian
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/autodock-vina/trunk/debian/README.Debian 2010-11-11 15:40:24 UTC (rev 5421)
@@ -0,0 +1,7 @@
+autodock-vina for Debian
+------------------------
+
+Users of this package may also be interested in the
+packages autodock and autogrid.
+
+ -- Yask Gupta <yask.gupta87 at gmail.com> Thu, 11 Nov 2010 15:52:17 +0100
Added: trunk/packages/autodock-vina/trunk/debian/README.source
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/README.source (rev 0)
+++ trunk/packages/autodock-vina/trunk/debian/README.source 2010-11-11 15:40:24 UTC (rev 5421)
@@ -0,0 +1,11 @@
+autodock-vina for Debian
+------------------------
+
+No changes were done to upstream's source code,
+just the name of the base directory adjusted
+to the Debian policy.
+
+The build process was adjusted according to
+http://vina.scripps.edu/manual.html#build
+and an otherwise missing Makefile added to
+allow the direct application of cdbs.
Added: trunk/packages/autodock-vina/trunk/debian/autodock-vina.doc-base.EX
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/autodock-vina.doc-base.EX (rev 0)
+++ trunk/packages/autodock-vina/trunk/debian/autodock-vina.doc-base.EX 2010-11-11 15:40:24 UTC (rev 5421)
@@ -0,0 +1,20 @@
+Document: autodock-vina
+Title: Debian autodock-vina Manual
+Author: <insert document author here>
+Abstract: This manual describes what autodock-vina is
+ and how it can be used to
+ manage online manuals on Debian systems.
+Section: unknown
+
+Format: debiandoc-sgml
+Files: /usr/share/doc/autodock-vina/autodock-vina.sgml.gz
+
+Format: postscript
+Files: /usr/share/doc/autodock-vina/autodock-vina.ps.gz
+
+Format: text
+Files: /usr/share/doc/autodock-vina/autodock-vina.text.gz
+
+Format: HTML
+Index: /usr/share/doc/autodock-vina/html/index.html
+Files: /usr/share/doc/autodock-vina/html/*.html
Added: trunk/packages/autodock-vina/trunk/debian/autodock-vina.install
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/autodock-vina.install (rev 0)
+++ trunk/packages/autodock-vina/trunk/debian/autodock-vina.install 2010-11-11 15:40:24 UTC (rev 5421)
@@ -0,0 +1,2 @@
+build/linux/release/vina usr/bin
+build/linux/release/vina_split usr/bin
Added: trunk/packages/autodock-vina/trunk/debian/changelog
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/changelog (rev 0)
+++ trunk/packages/autodock-vina/trunk/debian/changelog 2010-11-11 15:40:24 UTC (rev 5421)
@@ -0,0 +1,5 @@
+autodock-vina (1.1.1-1) experimental; urgency=low
+
+ * Initial release.
+
+ -- Yask Gupta <yask.gupta87 at gmail.com> Thu, 11 Nov 2010 15:52:17 +0100
Added: trunk/packages/autodock-vina/trunk/debian/compat
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/compat (rev 0)
+++ trunk/packages/autodock-vina/trunk/debian/compat 2010-11-11 15:40:24 UTC (rev 5421)
@@ -0,0 +1 @@
+7
Added: trunk/packages/autodock-vina/trunk/debian/control
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/control (rev 0)
+++ trunk/packages/autodock-vina/trunk/debian/control 2010-11-11 15:40:24 UTC (rev 5421)
@@ -0,0 +1,22 @@
+Source: autodock-vina
+Section: science
+Priority: extra
+Maintainer: Yask Gupta <yask.gupta87 at gmail.com>
+Build-Depends: debhelper (>= 7), libboost-all-dev
+Standards-Version: 3.9.1
+Homepage: http://vina.scripps.edu
+
+Package: autodock-vina
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: docking of small molecules to proteins
+ AutoDock Vina is a program to support drug discovery, molecular
+ docking and virtual screening of compound libraries. It offers
+ multi-core capability, high performance and enhanced accuracy
+ and ease of use.
+ .
+ The same institute also developed autodock, which is widely used.
+ .
+ O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy
+ of docking with a new scoring function, efficient optimization and
+ multithreading, Journal of Computational Chemistry 31 (2010) 455-461
Added: trunk/packages/autodock-vina/trunk/debian/copyright
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/copyright (rev 0)
+++ trunk/packages/autodock-vina/trunk/debian/copyright 2010-11-11 15:40:24 UTC (rev 5421)
@@ -0,0 +1,36 @@
+This work was packaged for Debian by:
+
+ Yask Gupta <yask.gupta87 at gmail.com> on Thu, 11 Nov 2010 15:52:17 +0100
+
+It was downloaded from <http://vina.scripps.edu>
+
+Upstream Author:
+
+ Oleg Trott <ot14 at columbia.edu>
+
+Copyright:
+
+ Copyright (C) 2006-2010, The Scripps Research Institute
+
+License:
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+
+On Debian systems, the complete text of the Apache version 2.0 license
+can be found in `/usr/share/common-licenses/Apache-2.0'.
+
+The Debian packaging is:
+
+ Copyright (C) 2010 Yask Gupta <yask.gupta87 at gmail.com>
+
+and is put under the same license.
Added: trunk/packages/autodock-vina/trunk/debian/manpage.1.ex
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/manpage.1.ex (rev 0)
+++ trunk/packages/autodock-vina/trunk/debian/manpage.1.ex 2010-11-11 15:40:24 UTC (rev 5421)
@@ -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 AUTODOCK-VINA SECTION "November 11, 2010"
+.\" 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
+autodock-vina \- program to do something
+.SH SYNOPSIS
+.B autodock-vina
+.RI [ options ] " files" ...
+.br
+.B bar
+.RI [ options ] " files" ...
+.SH DESCRIPTION
+This manual page documents briefly the
+.B autodock-vina
+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.
+\fBautodock-vina\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
+autodock-vina was written by <upstream author>.
+.PP
+This manual page was written by yask <yask.gupta87 at gmail.com>,
+for the Debian project (and may be used by others).
Added: trunk/packages/autodock-vina/trunk/debian/manpage.sgml.ex
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/manpage.sgml.ex (rev 0)
+++ trunk/packages/autodock-vina/trunk/debian/manpage.sgml.ex 2010-11-11 15:40:24 UTC (rev 5421)
@@ -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>November 11, 2010</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>yask.gupta87 at gmail.com</email>">
+ <!ENTITY dhusername "yask">
+ <!ENTITY dhucpackage "<refentrytitle>AUTODOCK-VINA</refentrytitle>">
+ <!ENTITY dhpackage "autodock-vina">
+
+ <!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/autodock-vina/trunk/debian/manpage.xml.ex
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/manpage.xml.ex (rev 0)
+++ trunk/packages/autodock-vina/trunk/debian/manpage.xml.ex 2010-11-11 15:40:24 UTC (rev 5421)
@@ -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 "yask">
+ <!ENTITY dhemail "yask.gupta87 at gmail.com">
+ <!-- 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 "autodock-vina User Manual">
+ <!ENTITY dhucpackage "AUTODOCK-VINA">
+ <!ENTITY dhpackage "autodock-vina">
+]>
+
+<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/autodock-vina/trunk/debian/patches/debian-changes-1.1.1-1
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/patches/debian-changes-1.1.1-1 (rev 0)
+++ trunk/packages/autodock-vina/trunk/debian/patches/debian-changes-1.1.1-1 2010-11-11 15:40:24 UTC (rev 5421)
@@ -0,0 +1,46 @@
+Description: Upstream changes introduced in version 1.1.1-1
+ 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:
+ .
+ autodock-vina (1.1.1-1) unstable; urgency=low
+ .
+ * Initial release (Closes: #nnnn)
+ .
+ The person named in the Author field signed this changelog entry.
+Author: Yask Gupta <yask.gupta87 at gmail.com>
+
+---
+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:
+
+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>
+
+--- /dev/null
++++ autodock-vina-1.1.1/\
+@@ -0,0 +1,19 @@
++#!/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 $@
++
++clean::
++ dh_clean
++ rm -f build/linux/release/*.o build/linux/release/vina*
++
++.PHONY: build
Added: trunk/packages/autodock-vina/trunk/debian/patches/series
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/patches/series (rev 0)
+++ trunk/packages/autodock-vina/trunk/debian/patches/series 2010-11-11 15:40:24 UTC (rev 5421)
@@ -0,0 +1,2 @@
+top_level_Makefile.patch
+debian-changes-1.1.1-1
Added: trunk/packages/autodock-vina/trunk/debian/patches/top_level_Makefile.patch
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/patches/top_level_Makefile.patch (rev 0)
+++ trunk/packages/autodock-vina/trunk/debian/patches/top_level_Makefile.patch 2010-11-11 15:40:24 UTC (rev 5421)
@@ -0,0 +1,8 @@
+Index: autodock-vina-1.1.1/Makefile
+===================================================================
+--- /dev/null 1970-01-01 00:00:00.000000000 +0000
++++ autodock-vina-1.1.1/Makefile 2010-11-11 16:08:04.869567044 +0100
+@@ -0,0 +1,3 @@
++
++all:
++ $(MAKE) BASE=/usr -C build/linux/release
Added: trunk/packages/autodock-vina/trunk/debian/rules
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/rules (rev 0)
+++ trunk/packages/autodock-vina/trunk/debian/rules 2010-11-11 15:40:24 UTC (rev 5421)
@@ -0,0 +1,19 @@
+#!/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 $@
+
+clean::
+ dh_clean
+ rm -f build/linux/release/*.o build/linux/release/vina*
+
+.PHONY: build
Property changes on: trunk/packages/autodock-vina/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/autodock-vina/trunk/debian/source/format
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/source/format (rev 0)
+++ trunk/packages/autodock-vina/trunk/debian/source/format 2010-11-11 15:40:24 UTC (rev 5421)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/autodock-vina/trunk/debian/watch
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/watch (rev 0)
+++ trunk/packages/autodock-vina/trunk/debian/watch 2010-11-11 15:40:24 UTC (rev 5421)
@@ -0,0 +1,4 @@
+version=3
+http://vina.scripps.edu/download/autodock_vina_([0-9_]*).tgz
+
+# Some good soul please help with the right watch line, please.
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