[med-svn] [snp-sites] 04/04: (Re)commit Jorge Sebastião Soares debian/ dir
Andreas Tille
tille at debian.org
Thu Dec 5 16:30:59 UTC 2013
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository snp-sites.
commit 64f577462bc5b6db4a8f76d89c6c8e8902815ecc
Author: Andreas Tille <tille at debian.org>
Date: Thu Dec 5 17:35:15 2013 +0100
(Re)commit Jorge Sebastião Soares debian/ dir
---
debian/README.Debian | 6 +
debian/README.source | 9 +
debian/changelog | 5 +
debian/compat | 1 +
debian/control | 40 +++
debian/copyright | 38 +++
debian/docs | 1 +
debian/emacsen-install.ex | 47 +++
debian/emacsen-remove.ex | 15 +
debian/emacsen-startup.ex | 27 ++
debian/init.d.ex | 154 ++++++++++
debian/libsnp-sites0-dev.install | 8 +
debian/libsnp-sites0.install | 1 +
debian/manpage.1.ex | 56 ++++
debian/manpage.sgml.ex | 154 ++++++++++
debian/manpage.xml.ex | 291 +++++++++++++++++++
debian/menu.ex | 2 +
debian/patches/added_specific_lib_to_libsnp-sites0 | 321 +++++++++++++++++++++
debian/patches/series | 1 +
debian/postinst.ex | 39 +++
debian/postrm.ex | 37 +++
debian/preinst.ex | 35 +++
debian/prerm.ex | 38 +++
debian/rules | 13 +
debian/snp-sites.cron.d.ex | 4 +
debian/snp-sites.default.ex | 10 +
debian/snp-sites.doc-base.EX | 20 ++
debian/snp-sites.install | 1 +
debian/source/format | 1 +
debian/watch.ex | 23 ++
30 files changed, 1398 insertions(+)
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..4389cc6
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,6 @@
+snp-sites for Debian
+--------------------
+
+<possible notes regarding this package - if none, delete this file>
+
+ -- Jorge Soares <js21 at sanger.ac.uk> Tue, 03 Dec 2013 11:52:54 +0000
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..3b91435
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,9 @@
+snp-sites 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>
+
+
+
+
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..26d460f
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+snp-sites (1-1) unstable; urgency=low
+
+ * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+
+ -- Jorge Soares <js21 at sanger.ac.uk> Tue, 03 Dec 2013 11:52:54 +0000
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..45a4fb7
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+8
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..9bd04ff
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,40 @@
+Source: snp-sites
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Jorge Soares <j.s.soares at gmail.com>
+Build-Depends: debhelper (>= 8.0.0),
+ autotools-dev,
+ zlib1g-dev,
+ check
+Standards-Version: 3.9.3
+Homepage: https://github.com/sanger-pathogens/snp_sites
+Vcs-Git: git://anonscm.debian.org/debian-med/snp-sites.git
+Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/snp-sites.git
+
+Package: snp-sites
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ zlib1g,
+ libsnp-sites0
+Description: This program finds snp sites from a multi fasta alignment file
+ This program finds snp sites from a multi fasta alignment file
+
+Package: libsnp-sites0
+Architecture: any
+Section: libs
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ zlib1g
+Description: This program finds snp sites from a multi fasta alignment file
+ This program finds snp sites from a multi fasta alignment file
+
+Package: libsnp-sites0-dev
+Architecture: any
+Section: libdevel
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ libsnp-sites0 (= ${binary:Version})
+Description: This program finds snp sites from a multi fasta alignment file
+ This program finds snp sites from a multi fasta alignment file
\ No newline at end of file
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..0e069ce
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,38 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: snp-sites
+Source: <url://example.com>
+
+Files: *
+Copyright: <years> <put author's name and email here>
+ <years> <likewise for another author>
+License: <special license>
+ <Put the license of the package here indented by 1 space>
+ <This follows the format of Description: lines in control file>
+ .
+ <Including paragraphs>
+
+# If you want to use GPL v2 or later for the /debian/* files use
+# the following clauses, or change it to suit. Delete these two lines
+Files: debian/*
+Copyright: 2013 Jorge Soares <js21 at sanger.ac.uk>
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+# Please also look if there are files or directories which have a
+# different copyright/license attached and list them here.
+# Please avoid to pick license terms that are more restrictive than the
+# packaged work, as it may make Debian's contributions unacceptable upstream.
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..b43bf86
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1 @@
+README.md
diff --git a/debian/emacsen-install.ex b/debian/emacsen-install.ex
new file mode 100644
index 0000000..72a2791
--- /dev/null
+++ b/debian/emacsen-install.ex
@@ -0,0 +1,47 @@
+#! /bin/sh -e
+# /usr/lib/emacsen-common/packages/install/snp-sites
+
+# Written by Jim Van Zandt <jrv at debian.org>, borrowing heavily
+# from the install scripts for gettext by Santiago Vila
+# <sanvila at ctv.es> and octave by Dirk Eddelbuettel <edd at debian.org>.
+
+FLAVOR=$1
+PACKAGE=snp-sites
+
+if [ ${FLAVOR} = emacs ]; then exit 0; fi
+
+echo install/${PACKAGE}: Handling install for emacsen flavor ${FLAVOR}
+
+#FLAVORTEST=`echo $FLAVOR | cut -c-6`
+#if [ ${FLAVORTEST} = xemacs ] ; then
+# SITEFLAG="-no-site-file"
+#else
+# SITEFLAG="--no-site-file"
+#fi
+FLAGS="${SITEFLAG} -q -batch -l path.el -f batch-byte-compile"
+
+ELDIR=/usr/share/emacs/site-lisp/${PACKAGE}
+ELCDIR=/usr/share/${FLAVOR}/site-lisp/${PACKAGE}
+ELRELDIR=../../../emacs/site-lisp/${PACKAGE}
+
+# Install-info-altdir does not actually exist.
+# Maybe somebody will write it.
+if test -x /usr/sbin/install-info-altdir; then
+ echo install/${PACKAGE}: install Info links for ${FLAVOR}
+ install-info-altdir --quiet --section "" "" --dirname=${FLAVOR} /usr/share/info/${PACKAGE}.info.gz
+fi
+
+install -m 755 -d ${ELCDIR}
+cd ${ELDIR}
+FILES=`echo *.el`
+cd ${ELCDIR}
+ln -sf ${ELRELDIR}/*.el .
+
+cat << EOF > path.el
+(debian-pkg-add-load-path-item ".")
+(setq byte-compile-warnings nil)
+EOF
+${FLAVOR} ${FLAGS} ${FILES}
+rm -f path.el
+
+exit 0
diff --git a/debian/emacsen-remove.ex b/debian/emacsen-remove.ex
new file mode 100644
index 0000000..cb10620
--- /dev/null
+++ b/debian/emacsen-remove.ex
@@ -0,0 +1,15 @@
+#!/bin/sh -e
+# /usr/lib/emacsen-common/packages/remove/snp-sites
+
+FLAVOR=$1
+PACKAGE=snp-sites
+
+if [ ${FLAVOR} != emacs ]; then
+ if test -x /usr/sbin/install-info-altdir; then
+ echo remove/${PACKAGE}: removing Info links for ${FLAVOR}
+ install-info-altdir --quiet --remove --dirname=${FLAVOR} /usr/share/info/snp-sites.info.gz
+ fi
+
+ echo remove/${PACKAGE}: purging byte-compiled files for ${FLAVOR}
+ rm -rf /usr/share/${FLAVOR}/site-lisp/${PACKAGE}
+fi
diff --git a/debian/emacsen-startup.ex b/debian/emacsen-startup.ex
new file mode 100644
index 0000000..c82cd6a
--- /dev/null
+++ b/debian/emacsen-startup.ex
@@ -0,0 +1,27 @@
+;; -*-emacs-lisp-*-
+;;
+;; Emacs startup file, e.g. /etc/emacs/site-start.d/50snp-sites.el
+;; for the Debian snp-sites package
+;;
+;; Originally contributed by Nils Naumann <naumann at unileoben.ac.at>
+;; Modified by Dirk Eddelbuettel <edd at debian.org>
+;; Adapted for dh-make by Jim Van Zandt <jrv at debian.org>
+
+;; The snp-sites package follows the Debian/GNU Linux 'emacsen' policy and
+;; byte-compiles its elisp files for each 'emacs flavor' (emacs19,
+;; xemacs19, emacs20, xemacs20...). The compiled code is then
+;; installed in a subdirectory of the respective site-lisp directory.
+;; We have to add this to the load-path:
+(let ((package-dir (concat "/usr/share/"
+ (symbol-name debian-emacs-flavor)
+ "/site-lisp/snp-sites")))
+;; If package-dir does not exist, the snp-sites package must have
+;; removed but not purged, and we should skip the setup.
+ (when (file-directory-p package-dir)
+ (if (fboundp 'debian-pkg-add-load-path-item)
+ (debian-pkg-add-load-path-item package-dir)
+ (setq load-path (cons package-dir load-path)))
+ (autoload 'snp-sites-mode "snp-sites-mode"
+ "Major mode for editing snp-sites files." t)
+ (add-to-list 'auto-mode-alist '("\\.snp-sites$" . snp-sites-mode))))
+
diff --git a/debian/init.d.ex b/debian/init.d.ex
new file mode 100644
index 0000000..f0a89d9
--- /dev/null
+++ b/debian/init.d.ex
@@ -0,0 +1,154 @@
+#!/bin/sh
+### BEGIN INIT INFO
+# Provides: snp-sites
+# Required-Start: $network $local_fs
+# Required-Stop:
+# Default-Start: 2 3 4 5
+# Default-Stop: 0 1 6
+# Short-Description: <Enter a short description of the software>
+# Description: <Enter a long description of the software>
+# <...>
+# <...>
+### END INIT INFO
+
+# Author: Jorge Soares <js21 at sanger.ac.uk>
+
+# PATH should only include /usr/* if it runs after the mountnfs.sh script
+PATH=/sbin:/usr/sbin:/bin:/usr/bin
+DESC=snp-sites # Introduce a short description here
+NAME=snp-sites # Introduce the short server's name here
+DAEMON=/usr/sbin/snp-sites # Introduce the server's location here
+DAEMON_ARGS="" # Arguments to run the daemon with
+PIDFILE=/var/run/$NAME.pid
+SCRIPTNAME=/etc/init.d/$NAME
+
+# Exit if the package is not installed
+[ -x $DAEMON ] || exit 0
+
+# Read configuration variable file if it is present
+[ -r /etc/default/$NAME ] && . /etc/default/$NAME
+
+# Load the VERBOSE setting and other rcS variables
+. /lib/init/vars.sh
+
+# Define LSB log_* functions.
+# Depend on lsb-base (>= 3.0-6) to ensure that this file is present.
+. /lib/lsb/init-functions
+
+#
+# Function that starts the daemon/service
+#
+do_start()
+{
+ # Return
+ # 0 if daemon has been started
+ # 1 if daemon was already running
+ # 2 if daemon could not be started
+ start-stop-daemon --start --quiet --pidfile $PIDFILE --exec $DAEMON --test > /dev/null \
+ || return 1
+ start-stop-daemon --start --quiet --pidfile $PIDFILE --exec $DAEMON -- \
+ $DAEMON_ARGS \
+ || return 2
+ # Add code here, if necessary, that waits for the process to be ready
+ # to handle requests from services started subsequently which depend
+ # on this one. As a last resort, sleep for some time.
+}
+
+#
+# Function that stops the daemon/service
+#
+do_stop()
+{
+ # Return
+ # 0 if daemon has been stopped
+ # 1 if daemon was already stopped
+ # 2 if daemon could not be stopped
+ # other if a failure occurred
+ start-stop-daemon --stop --quiet --retry=TERM/30/KILL/5 --pidfile $PIDFILE --name $NAME
+ RETVAL="$?"
+ [ "$RETVAL" = 2 ] && return 2
+ # Wait for children to finish too if this is a daemon that forks
+ # and if the daemon is only ever run from this initscript.
+ # If the above conditions are not satisfied then add some other code
+ # that waits for the process to drop all resources that could be
+ # needed by services started subsequently. A last resort is to
+ # sleep for some time.
+ start-stop-daemon --stop --quiet --oknodo --retry=0/30/KILL/5 --exec $DAEMON
+ [ "$?" = 2 ] && return 2
+ # Many daemons don't delete their pidfiles when they exit.
+ rm -f $PIDFILE
+ return "$RETVAL"
+}
+
+#
+# Function that sends a SIGHUP to the daemon/service
+#
+do_reload() {
+ #
+ # If the daemon can reload its configuration without
+ # restarting (for example, when it is sent a SIGHUP),
+ # then implement that here.
+ #
+ start-stop-daemon --stop --signal 1 --quiet --pidfile $PIDFILE --name $NAME
+ return 0
+}
+
+case "$1" in
+ start)
+ [ "$VERBOSE" != no ] && log_daemon_msg "Starting $DESC " "$NAME"
+ do_start
+ case "$?" in
+ 0|1) [ "$VERBOSE" != no ] && log_end_msg 0 ;;
+ 2) [ "$VERBOSE" != no ] && log_end_msg 1 ;;
+ esac
+ ;;
+ stop)
+ [ "$VERBOSE" != no ] && log_daemon_msg "Stopping $DESC" "$NAME"
+ do_stop
+ case "$?" in
+ 0|1) [ "$VERBOSE" != no ] && log_end_msg 0 ;;
+ 2) [ "$VERBOSE" != no ] && log_end_msg 1 ;;
+ esac
+ ;;
+ status)
+ status_of_proc "$DAEMON" "$NAME" && exit 0 || exit $?
+ ;;
+ #reload|force-reload)
+ #
+ # If do_reload() is not implemented then leave this commented out
+ # and leave 'force-reload' as an alias for 'restart'.
+ #
+ #log_daemon_msg "Reloading $DESC" "$NAME"
+ #do_reload
+ #log_end_msg $?
+ #;;
+ restart|force-reload)
+ #
+ # If the "reload" option is implemented then remove the
+ # 'force-reload' alias
+ #
+ log_daemon_msg "Restarting $DESC" "$NAME"
+ do_stop
+ case "$?" in
+ 0|1)
+ do_start
+ case "$?" in
+ 0) log_end_msg 0 ;;
+ 1) log_end_msg 1 ;; # Old process is still running
+ *) log_end_msg 1 ;; # Failed to start
+ esac
+ ;;
+ *)
+ # Failed to stop
+ log_end_msg 1
+ ;;
+ esac
+ ;;
+ *)
+ #echo "Usage: $SCRIPTNAME {start|stop|restart|reload|force-reload}" >&2
+ echo "Usage: $SCRIPTNAME {start|stop|status|restart|force-reload}" >&2
+ exit 3
+ ;;
+esac
+
+:
diff --git a/debian/libsnp-sites0-dev.install b/debian/libsnp-sites0-dev.install
new file mode 100644
index 0000000..b6ea97b
--- /dev/null
+++ b/debian/libsnp-sites0-dev.install
@@ -0,0 +1,8 @@
+usr/share/parse_phylip.h usr/include/snp_sites/parse_phylip.h
+usr/share/vcf.h usr/include/snp_sites/vcf.h
+usr/share/kseq.h usr/include/snp_sites/kseq.h
+usr/share/fasta_of_snp_sites.h usr/include/snp_sites/fasta_of_snp_sites.h
+usr/share/phylib_of_snp_sites.h usr/include/snp_sites/phylib_of_snp_sites.h
+usr/share/snp_sites.h usr/include/snp_sites/snp_sites.h
+usr/share/alignment_file.h usr/include/snp_sites/alignment_file.h
+usr/share/string_cat.h usr/include/snp_sites/string_cat.h
\ No newline at end of file
diff --git a/debian/libsnp-sites0.install b/debian/libsnp-sites0.install
new file mode 100644
index 0000000..de3d642
--- /dev/null
+++ b/debian/libsnp-sites0.install
@@ -0,0 +1 @@
+usr/lib/
\ No newline at end of file
diff --git a/debian/manpage.1.ex b/debian/manpage.1.ex
new file mode 100644
index 0000000..f9c0b64
--- /dev/null
+++ b/debian/manpage.1.ex
@@ -0,0 +1,56 @@
+.\" Hey, EMACS: -*- nroff -*-
+.\" (C) Copyright 2013 Jorge Soares <js21 at sanger.ac.uk>,
+.\"
+.\" 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 SNP-SITES SECTION "December 5, 2013"
+.\" 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
+snp-sites \- program to do something
+.SH SYNOPSIS
+.B snp-sites
+.RI [ options ] " files" ...
+.br
+.B bar
+.RI [ options ] " files" ...
+.SH DESCRIPTION
+This manual page documents briefly the
+.B snp-sites
+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.
+\fBsnp-sites\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.
diff --git a/debian/manpage.sgml.ex b/debian/manpage.sgml.ex
new file mode 100644
index 0000000..11131cb
--- /dev/null
+++ b/debian/manpage.sgml.ex
@@ -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>December 5, 2013</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>js21 at sanger.ac.uk</email>">
+ <!ENTITY dhusername "Jorge Soares">
+ <!ENTITY dhucpackage "<refentrytitle>SNP-SITES</refentrytitle>">
+ <!ENTITY dhpackage "snp-sites">
+
+ <!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:
+-->
diff --git a/debian/manpage.xml.ex b/debian/manpage.xml.ex
new file mode 100644
index 0000000..cc42da1
--- /dev/null
+++ b/debian/manpage.xml.ex
@@ -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/docbook-xsl/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/docbook-xsl/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 "Jorge Soares">
+ <!ENTITY dhemail "js21 at sanger.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 "snp-sites User Manual">
+ <!ENTITY dhucpackage "SNP-SITES">
+ <!ENTITY dhpackage "snp-sites">
+]>
+
+<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>ENVIRONMENT</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>
+
diff --git a/debian/menu.ex b/debian/menu.ex
new file mode 100644
index 0000000..0003047
--- /dev/null
+++ b/debian/menu.ex
@@ -0,0 +1,2 @@
+?package(snp-sites):needs="X11|text|vc|wm" section="Applications/see-menu-manual"\
+ title="snp-sites" command="/usr/bin/snp-sites"
diff --git a/debian/patches/added_specific_lib_to_libsnp-sites0 b/debian/patches/added_specific_lib_to_libsnp-sites0
new file mode 100644
index 0000000..bf6ab38
--- /dev/null
+++ b/debian/patches/added_specific_lib_to_libsnp-sites0
@@ -0,0 +1,321 @@
+Description: <short summary of the patch>
+ TODO: Put a short summary on the line above and replace this paragraph
+ with a longer explanation of this change. Complete the meta-information
+ with other relevant fields (see below for details). To make it easier, the
+ information below has been extracted from the changelog. Adjust it or drop
+ it.
+ .
+ snp-sites (1-1) unstable; urgency=low
+ .
+ * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+Author: Jorge Soares <js21 at sanger.ac.uk>
+
+---
+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>
+Bug-Ubuntu: https://launchpad.net/bugs/<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
++++ snp-sites-1/config.log
+@@ -0,0 +1,293 @@
++This file contains any messages produced by compilers while
++running configure, to aid debugging if configure makes a mistake.
++
++It was created by snp_sites configure 1, which was
++generated by GNU Autoconf 2.69. Invocation command line was
++
++ $ ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=${prefix}/include --mandir=${prefix}/share/man --infodir=${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --libexecdir=${prefix}/lib/snp-sites --disable-maintainer-mode --disable-dependency-tracking
++
++## --------- ##
++## Platform. ##
++## --------- ##
++
++hostname = builder
++uname -m = x86_64
++uname -r = 3.2.0-4-amd64
++uname -s = Linux
++uname -v = #1 SMP Debian 3.2.51-1
++
++/usr/bin/uname -p = unknown
++/bin/uname -X = unknown
++
++/bin/arch = unknown
++/usr/bin/arch -k = unknown
++/usr/convex/getsysinfo = unknown
++/usr/bin/hostinfo = unknown
++/bin/machine = unknown
++/usr/bin/oslevel = unknown
++/bin/universe = unknown
++
++PATH: /usr/local/bin
++PATH: /usr/bin
++PATH: /bin
++PATH: /usr/local/games
++PATH: /usr/games
++
++
++## ----------- ##
++## Core tests. ##
++## ----------- ##
++
++configure:2369: checking for a BSD-compatible install
++configure:2437: result: /usr/bin/install -c
++configure:2448: checking whether build environment is sane
++configure:2498: result: yes
++configure:2639: checking for a thread-safe mkdir -p
++configure:2678: result: /bin/mkdir -p
++configure:2691: checking for gawk
++configure:2721: result: no
++configure:2691: checking for mawk
++configure:2707: found /usr/bin/mawk
++configure:2718: result: mawk
++configure:2729: checking whether make sets $(MAKE)
++configure:2751: result: yes
++configure:2865: checking build system type
++configure:2879: result: x86_64-pc-linux-gnu
++configure:2899: checking host system type
++configure:2912: result: x86_64-pc-linux-gnu
++configure:2953: checking how to print strings
++configure:2980: result: printf
++configure:3013: checking for style of include used by make
++configure:3041: result: GNU
++configure:3112: checking for gcc
++configure:3128: found /usr/bin/gcc
++configure:3139: result: gcc
++configure:3368: checking for C compiler version
++configure:3377: gcc --version >&5
++gcc (Debian 4.7.2-5) 4.7.2
++Copyright (C) 2012 Free Software Foundation, Inc.
++This is free software; see the source for copying conditions. There is NO
++warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
++
++configure:3388: $? = 0
++configure:3377: gcc -v >&5
++Using built-in specs.
++COLLECT_GCC=gcc
++COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.7/lto-wrapper
++Target: x86_64-linux-gnu
++Configured with: ../src/configure -v --with-pkgversion='Debian 4.7.2-5' --with-bugurl=file:///usr/share/doc/gcc-4.7/README.Bugs --enable-languages=c,c++,go,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.7 --enable-shared --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.7 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable [...]
++Thread model: posix
++gcc version 4.7.2 (Debian 4.7.2-5)
++configure:3388: $? = 0
++configure:3377: gcc -V >&5
++gcc: error: unrecognized command line option '-V'
++gcc: fatal error: no input files
++compilation terminated.
++configure:3388: $? = 4
++configure:3377: gcc -qversion >&5
++gcc: error: unrecognized command line option '-qversion'
++gcc: fatal error: no input files
++compilation terminated.
++configure:3388: $? = 4
++configure:3408: checking whether the C compiler works
++configure:3430: gcc conftest.c >&5
++configure:3434: $? = 0
++configure:3482: result: yes
++configure:3485: checking for C compiler default output file name
++configure:3487: result: a.out
++configure:3493: checking for suffix of executables
++configure:3500: gcc -o conftest conftest.c >&5
++configure:3504: $? = 0
++configure:3526: result:
++configure:3548: checking whether we are cross compiling
++configure:3556: gcc -o conftest conftest.c >&5
++configure:3560: $? = 0
++configure:3567: ./conftest
++configure:3571: $? = 0
++configure:3586: result: no
++configure:3591: checking for suffix of object files
++configure:3613: gcc -c conftest.c >&5
++configure:3617: $? = 0
++configure:3638: result: o
++configure:3642: checking whether we are using the GNU C compiler
++configure:3661: gcc -c conftest.c >&5
++
++## ---------------- ##
++## Cache variables. ##
++## ---------------- ##
++
++ac_cv_build=x86_64-pc-linux-gnu
++ac_cv_env_CCC_set=
++ac_cv_env_CCC_value=
++ac_cv_env_CC_set=
++ac_cv_env_CC_value=
++ac_cv_env_CFLAGS_set=
++ac_cv_env_CFLAGS_value=
++ac_cv_env_CPPFLAGS_set=
++ac_cv_env_CPPFLAGS_value=
++ac_cv_env_CPP_set=
++ac_cv_env_CPP_value=
++ac_cv_env_CXXCPP_set=
++ac_cv_env_CXXCPP_value=
++ac_cv_env_CXXFLAGS_set=
++ac_cv_env_CXXFLAGS_value=
++ac_cv_env_CXX_set=
++ac_cv_env_CXX_value=
++ac_cv_env_LDFLAGS_set=
++ac_cv_env_LDFLAGS_value=
++ac_cv_env_LIBS_set=
++ac_cv_env_LIBS_value=
++ac_cv_env_build_alias_set=set
++ac_cv_env_build_alias_value=x86_64-linux-gnu
++ac_cv_env_host_alias_set=
++ac_cv_env_host_alias_value=
++ac_cv_env_target_alias_set=
++ac_cv_env_target_alias_value=
++ac_cv_host=x86_64-pc-linux-gnu
++ac_cv_objext=o
++ac_cv_path_install='/usr/bin/install -c'
++ac_cv_path_mkdir=/bin/mkdir
++ac_cv_prog_AWK=mawk
++ac_cv_prog_ac_ct_CC=gcc
++ac_cv_prog_make_make_set=yes
++
++## ----------------- ##
++## Output variables. ##
++## ----------------- ##
++
++ACLOCAL='${SHELL} /home/js21/deb_package_creation/snp_sites-1/missing --run aclocal-1.11'
++AMDEPBACKSLASH=''
++AMDEP_FALSE=''
++AMDEP_TRUE='#'
++AMTAR='$${TAR-tar}'
++AR=''
++AUTOCONF='${SHELL} /home/js21/deb_package_creation/snp_sites-1/missing --run autoconf'
++AUTOHEADER='${SHELL} /home/js21/deb_package_creation/snp_sites-1/missing --run autoheader'
++AUTOMAKE='${SHELL} /home/js21/deb_package_creation/snp_sites-1/missing --run automake-1.11'
++AWK='mawk'
++CC='gcc'
++CCDEPMODE=''
++CFLAGS=''
++CPP=''
++CPPFLAGS=''
++CXX=''
++CXXCPP=''
++CXXDEPMODE=''
++CXXFLAGS=''
++CYGPATH_W='echo'
++DEFS=''
++DEPDIR='.deps'
++DLLTOOL=''
++DSYMUTIL=''
++DUMPBIN=''
++ECHO_C=''
++ECHO_N='-n'
++ECHO_T=''
++EGREP=''
++EXEEXT=''
++FGREP=''
++GREP=''
++INSTALL_DATA='${INSTALL} -m 644'
++INSTALL_PROGRAM='${INSTALL}'
++INSTALL_SCRIPT='${INSTALL}'
++INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
++LD=''
++LDFLAGS=''
++LIBOBJS=''
++LIBS=''
++LIBTOOL=''
++LIPO=''
++LN_S=''
++LTLIBOBJS=''
++MAKEINFO='${SHELL} /home/js21/deb_package_creation/snp_sites-1/missing --run makeinfo'
++MANIFEST_TOOL=''
++MKDIR_P='/bin/mkdir -p'
++NM=''
++NMEDIT=''
++OBJDUMP=''
++OBJEXT='o'
++OTOOL64=''
++OTOOL=''
++PACKAGE='snp_sites'
++PACKAGE_BUGREPORT=''
++PACKAGE_NAME='snp_sites'
++PACKAGE_STRING='snp_sites 1'
++PACKAGE_TARNAME='snp_sites'
++PACKAGE_URL=''
++PACKAGE_VERSION='1'
++PATH_SEPARATOR=':'
++RANLIB=''
++SED=''
++SET_MAKE=''
++SHELL='/bin/bash'
++STRIP=''
++VERSION='1'
++ac_ct_AR=''
++ac_ct_CC='gcc'
++ac_ct_CXX=''
++ac_ct_DUMPBIN=''
++am__EXEEXT_FALSE=''
++am__EXEEXT_TRUE=''
++am__fastdepCC_FALSE=''
++am__fastdepCC_TRUE=''
++am__fastdepCXX_FALSE=''
++am__fastdepCXX_TRUE=''
++am__include='include'
++am__isrc=''
++am__leading_dot='.'
++am__nodep=''
++am__quote=''
++am__tar='$${TAR-tar} chof - "$$tardir"'
++am__untar='$${TAR-tar} xf -'
++bindir='${exec_prefix}/bin'
++build='x86_64-pc-linux-gnu'
++build_alias='x86_64-linux-gnu'
++build_cpu='x86_64'
++build_os='linux-gnu'
++build_vendor='pc'
++datadir='${datarootdir}'
++datarootdir='${prefix}/share'
++docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
++dvidir='${docdir}'
++exec_prefix='NONE'
++host='x86_64-pc-linux-gnu'
++host_alias=''
++host_cpu='x86_64'
++host_os='linux-gnu'
++host_vendor='pc'
++htmldir='${docdir}'
++includedir='${prefix}/include'
++infodir='${prefix}/share/info'
++install_sh='${SHELL} /home/js21/deb_package_creation/snp_sites-1/install-sh'
++libdir='${exec_prefix}/lib'
++libexecdir='${prefix}/lib/snp-sites'
++localedir='${datarootdir}/locale'
++localstatedir='/var'
++mandir='${prefix}/share/man'
++mkdir_p='/bin/mkdir -p'
++oldincludedir='/usr/include'
++pdfdir='${docdir}'
++prefix='/usr'
++program_transform_name='s,x,x,'
++psdir='${docdir}'
++sbindir='${exec_prefix}/sbin'
++sharedstatedir='${prefix}/com'
++sysconfdir='/etc'
++target_alias=''
++
++## ----------- ##
++## confdefs.h. ##
++## ----------- ##
++
++/* confdefs.h */
++#define PACKAGE_NAME "snp_sites"
++#define PACKAGE_TARNAME "snp_sites"
++#define PACKAGE_VERSION "1"
++#define PACKAGE_STRING "snp_sites 1"
++#define PACKAGE_BUGREPORT ""
++#define PACKAGE_URL ""
++#define PACKAGE "snp_sites"
++#define VERSION "1"
++
++configure: caught signal 2
++configure: exit 1
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..9ad1994
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+added_specific_lib_to_libsnp-sites0
diff --git a/debian/postinst.ex b/debian/postinst.ex
new file mode 100644
index 0000000..021adbd
--- /dev/null
+++ b/debian/postinst.ex
@@ -0,0 +1,39 @@
+#!/bin/sh
+# postinst script for snp-sites
+#
+# see: dh_installdeb(1)
+
+set -e
+
+# summary of how this script can be called:
+# * <postinst> `configure' <most-recently-configured-version>
+# * <old-postinst> `abort-upgrade' <new version>
+# * <conflictor's-postinst> `abort-remove' `in-favour' <package>
+# <new-version>
+# * <postinst> `abort-remove'
+# * <deconfigured's-postinst> `abort-deconfigure' `in-favour'
+# <failed-install-package> <version> `removing'
+# <conflicting-package> <version>
+# for details, see http://www.debian.org/doc/debian-policy/ or
+# the debian-policy package
+
+
+case "$1" in
+ configure)
+ ;;
+
+ abort-upgrade|abort-remove|abort-deconfigure)
+ ;;
+
+ *)
+ echo "postinst called with unknown argument \`$1'" >&2
+ exit 1
+ ;;
+esac
+
+# dh_installdeb will replace this with shell code automatically
+# generated by other debhelper scripts.
+
+#DEBHELPER#
+
+exit 0
diff --git a/debian/postrm.ex b/debian/postrm.ex
new file mode 100644
index 0000000..b9a7fdc
--- /dev/null
+++ b/debian/postrm.ex
@@ -0,0 +1,37 @@
+#!/bin/sh
+# postrm script for snp-sites
+#
+# see: dh_installdeb(1)
+
+set -e
+
+# summary of how this script can be called:
+# * <postrm> `remove'
+# * <postrm> `purge'
+# * <old-postrm> `upgrade' <new-version>
+# * <new-postrm> `failed-upgrade' <old-version>
+# * <new-postrm> `abort-install'
+# * <new-postrm> `abort-install' <old-version>
+# * <new-postrm> `abort-upgrade' <old-version>
+# * <disappearer's-postrm> `disappear' <overwriter>
+# <overwriter-version>
+# for details, see http://www.debian.org/doc/debian-policy/ or
+# the debian-policy package
+
+
+case "$1" in
+ purge|remove|upgrade|failed-upgrade|abort-install|abort-upgrade|disappear)
+ ;;
+
+ *)
+ echo "postrm called with unknown argument \`$1'" >&2
+ exit 1
+ ;;
+esac
+
+# dh_installdeb will replace this with shell code automatically
+# generated by other debhelper scripts.
+
+#DEBHELPER#
+
+exit 0
diff --git a/debian/preinst.ex b/debian/preinst.ex
new file mode 100644
index 0000000..8f51365
--- /dev/null
+++ b/debian/preinst.ex
@@ -0,0 +1,35 @@
+#!/bin/sh
+# preinst script for snp-sites
+#
+# see: dh_installdeb(1)
+
+set -e
+
+# summary of how this script can be called:
+# * <new-preinst> `install'
+# * <new-preinst> `install' <old-version>
+# * <new-preinst> `upgrade' <old-version>
+# * <old-preinst> `abort-upgrade' <new-version>
+# for details, see http://www.debian.org/doc/debian-policy/ or
+# the debian-policy package
+
+
+case "$1" in
+ install|upgrade)
+ ;;
+
+ abort-upgrade)
+ ;;
+
+ *)
+ echo "preinst called with unknown argument \`$1'" >&2
+ exit 1
+ ;;
+esac
+
+# dh_installdeb will replace this with shell code automatically
+# generated by other debhelper scripts.
+
+#DEBHELPER#
+
+exit 0
diff --git a/debian/prerm.ex b/debian/prerm.ex
new file mode 100644
index 0000000..f33b8d2
--- /dev/null
+++ b/debian/prerm.ex
@@ -0,0 +1,38 @@
+#!/bin/sh
+# prerm script for snp-sites
+#
+# see: dh_installdeb(1)
+
+set -e
+
+# summary of how this script can be called:
+# * <prerm> `remove'
+# * <old-prerm> `upgrade' <new-version>
+# * <new-prerm> `failed-upgrade' <old-version>
+# * <conflictor's-prerm> `remove' `in-favour' <package> <new-version>
+# * <deconfigured's-prerm> `deconfigure' `in-favour'
+# <package-being-installed> <version> `removing'
+# <conflicting-package> <version>
+# for details, see http://www.debian.org/doc/debian-policy/ or
+# the debian-policy package
+
+
+case "$1" in
+ remove|upgrade|deconfigure)
+ ;;
+
+ failed-upgrade)
+ ;;
+
+ *)
+ echo "prerm called with unknown argument \`$1'" >&2
+ exit 1
+ ;;
+esac
+
+# dh_installdeb will replace this with shell code automatically
+# generated by other debhelper scripts.
+
+#DEBHELPER#
+
+exit 0
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..b760bee
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,13 @@
+#!/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 $@
diff --git a/debian/snp-sites.cron.d.ex b/debian/snp-sites.cron.d.ex
new file mode 100644
index 0000000..d652d97
--- /dev/null
+++ b/debian/snp-sites.cron.d.ex
@@ -0,0 +1,4 @@
+#
+# Regular cron jobs for the snp-sites package
+#
+0 4 * * * root [ -x /usr/bin/snp-sites_maintenance ] && /usr/bin/snp-sites_maintenance
diff --git a/debian/snp-sites.default.ex b/debian/snp-sites.default.ex
new file mode 100644
index 0000000..e8687bb
--- /dev/null
+++ b/debian/snp-sites.default.ex
@@ -0,0 +1,10 @@
+# Defaults for snp-sites initscript
+# sourced by /etc/init.d/snp-sites
+# installed at /etc/default/snp-sites by the maintainer scripts
+
+#
+# This is a POSIX shell fragment
+#
+
+# Additional options that are passed to the Daemon.
+DAEMON_OPTS=""
diff --git a/debian/snp-sites.doc-base.EX b/debian/snp-sites.doc-base.EX
new file mode 100644
index 0000000..a3c9770
--- /dev/null
+++ b/debian/snp-sites.doc-base.EX
@@ -0,0 +1,20 @@
+Document: snp-sites
+Title: Debian snp-sites Manual
+Author: <insert document author here>
+Abstract: This manual describes what snp-sites is
+ and how it can be used to
+ manage online manuals on Debian systems.
+Section: unknown
+
+Format: debiandoc-sgml
+Files: /usr/share/doc/snp-sites/snp-sites.sgml.gz
+
+Format: postscript
+Files: /usr/share/doc/snp-sites/snp-sites.ps.gz
+
+Format: text
+Files: /usr/share/doc/snp-sites/snp-sites.text.gz
+
+Format: HTML
+Index: /usr/share/doc/snp-sites/html/index.html
+Files: /usr/share/doc/snp-sites/html/*.html
diff --git a/debian/snp-sites.install b/debian/snp-sites.install
new file mode 100644
index 0000000..368a69d
--- /dev/null
+++ b/debian/snp-sites.install
@@ -0,0 +1 @@
+usr/bin/snp_sites
\ No newline at end of file
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/watch.ex b/debian/watch.ex
new file mode 100644
index 0000000..03d3bd7
--- /dev/null
+++ b/debian/watch.ex
@@ -0,0 +1,23 @@
+# 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://www.example.com/downloads.php snp-sites-(.*)\.tar\.gz
+
+# Uncomment to examine a Webserver directory
+#http://www.example.com/pub/snp-sites-(.*)\.tar\.gz
+
+# Uncommment to examine a FTP server
+#ftp://ftp.example.com/pub/snp-sites-(.*)\.tar\.gz debian uupdate
+
+# Uncomment to find new files on sourceforge, for devscripts >= 2.9
+# http://sf.net/snp-sites/snp-sites-(.*)\.tar\.gz
+
+# Uncomment to find new files on GooglePages
+# http://example.googlepages.com/foo.html snp-sites-(.*)\.tar\.gz
--
Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/snp-sites.git
More information about the debian-med-commit
mailing list