[med-svn] [jbrowse] 01/09: Initial shot a jbrowse
Andreas Tille
tille at debian.org
Fri Dec 8 21:45:33 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository jbrowse.
commit cb311eb0afcffc7f1c884173bcf9ed7106b6973e
Author: Steffen Moeller <moeller at debian.org>
Date: Thu Jul 14 16:59:07 2011 +0000
Initial shot a jbrowse
---
debian/README.Debian | 6 +
debian/README.source | 9 ++
debian/changelog | 5 +
debian/compat | 1 +
debian/control | 15 ++
debian/copyright | 32 +++++
debian/docs | 1 +
debian/init.d.ex | 154 +++++++++++++++++++++
debian/jbrowse.cron.d.ex | 4 +
debian/jbrowse.default.ex | 10 ++
debian/jbrowse.dirs | 1 +
debian/jbrowse.doc-base.EX | 20 +++
debian/jbrowse.install | 17 +++
debian/manpage.1.ex | 59 ++++++++
debian/manpage.sgml.ex | 154 +++++++++++++++++++++
debian/manpage.xml.ex | 291 +++++++++++++++++++++++++++++++++++++++
debian/menu.ex | 2 +
debian/patches/clean_patch.patch | 13 ++
debian/patches/series | 1 +
debian/postinst.ex | 39 ++++++
debian/postrm.ex | 37 +++++
debian/preinst.ex | 35 +++++
debian/prerm.ex | 38 +++++
debian/rules | 13 ++
debian/source/format | 1 +
debian/watch.ex | 23 ++++
26 files changed, 981 insertions(+)
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..82e3985
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,6 @@
+jbrowse for Debian
+------------------
+
+<possible notes regarding this package - if none, delete this file>
+
+ -- Steffen Moeller <moeller at debian.org> Thu, 14 Jul 2011 18:38:37 +0200
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..93f0dda
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,9 @@
+jbrowse 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..fe60f3b
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+jbrowse (1.2.1-1) unstable; urgency=low
+
+ * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+
+ -- Steffen Moeller <moeller at debian.org> Thu, 14 Jul 2011 18:38:37 +0200
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..3b4d410
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,15 @@
+Source: jbrowse
+Section: science
+Priority: extra
+Maintainer: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 8.0.0), autotools-dev
+Standards-Version: 3.9.2
+Homepage: http://www.jbrowse.org
+#Vcs-Git: git://git.debian.org/collab-maint/jbrowse.git
+#Vcs-Browser: http://git.debian.org/?p=collab-maint/jbrowse.git;a=summary
+
+Package: jbrowse
+Architecture: any
+Depends: ${misc:Depends}, apache2, bioperl
+Description: genome browser
+ <insert long description, indented with spaces>
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..b05a23a
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,32 @@
+Format: http://dep.debian.net/deps/dep5
+Upstream-Name: jbrowse
+Source: <url://example.com>
+
+Files: *
+Copyright: <years> <put author's name and email here>
+ <years> <likewise for another author>
+License: GPL-3.0+
+
+Files: debian/*
+Copyright: 2011 Steffen Moeller <moeller at debian.org>
+License: GPL-3.0+
+
+License: GPL-3.0+
+ This program 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 3 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 3 can be found in "/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.
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..2097443
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1 @@
+release-notes.txt
diff --git a/debian/init.d.ex b/debian/init.d.ex
new file mode 100644
index 0000000..c7f4fe3
--- /dev/null
+++ b/debian/init.d.ex
@@ -0,0 +1,154 @@
+#!/bin/sh
+### BEGIN INIT INFO
+# Provides: jbrowse
+# Required-Start: $network $local_fs
+# Required-Stop:
+# Default-Start: 2 3 4 5
+# Default-Stop: 0 1 6
+# Short-Description: <Enter a short description of the sortware>
+# Description: <Enter a long description of the software>
+# <...>
+# <...>
+### END INIT INFO
+
+# Author: Steffen Moeller <moeller at debian.org>
+
+# PATH should only include /usr/* if it runs after the mountnfs.sh script
+PATH=/sbin:/usr/sbin:/bin:/usr/bin
+DESC=jbrowse # Introduce a short description here
+NAME=jbrowse # Introduce the short server's name here
+DAEMON=/usr/sbin/jbrowse # Introduce the server's location here
+DAEMON_ARGS="" # Arguments to run the daemon with
+PIDFILE=/var/run/$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/jbrowse.cron.d.ex b/debian/jbrowse.cron.d.ex
new file mode 100644
index 0000000..b0fe9be
--- /dev/null
+++ b/debian/jbrowse.cron.d.ex
@@ -0,0 +1,4 @@
+#
+# Regular cron jobs for the jbrowse package
+#
+0 4 * * * root [ -x /usr/bin/jbrowse_maintenance ] && /usr/bin/jbrowse_maintenance
diff --git a/debian/jbrowse.default.ex b/debian/jbrowse.default.ex
new file mode 100644
index 0000000..a607b01
--- /dev/null
+++ b/debian/jbrowse.default.ex
@@ -0,0 +1,10 @@
+# Defaults for jbrowse initscript
+# sourced by /etc/init.d/jbrowse
+# installed at /etc/default/jbrowse by the maintainer scripts
+
+#
+# This is a POSIX shell fragment
+#
+
+# Additional options that are passed to the Daemon.
+DAEMON_OPTS=""
diff --git a/debian/jbrowse.dirs b/debian/jbrowse.dirs
new file mode 100644
index 0000000..5142711
--- /dev/null
+++ b/debian/jbrowse.dirs
@@ -0,0 +1 @@
+/var/www/jbrowse
diff --git a/debian/jbrowse.doc-base.EX b/debian/jbrowse.doc-base.EX
new file mode 100644
index 0000000..4055c88
--- /dev/null
+++ b/debian/jbrowse.doc-base.EX
@@ -0,0 +1,20 @@
+Document: jbrowse
+Title: Debian jbrowse Manual
+Author: <insert document author here>
+Abstract: This manual describes what jbrowse is
+ and how it can be used to
+ manage online manuals on Debian systems.
+Section: unknown
+
+Format: debiandoc-sgml
+Files: /usr/share/doc/jbrowse/jbrowse.sgml.gz
+
+Format: postscript
+Files: /usr/share/doc/jbrowse/jbrowse.ps.gz
+
+Format: text
+Files: /usr/share/doc/jbrowse/jbrowse.text.gz
+
+Format: HTML
+Index: /usr/share/doc/jbrowse/html/index.html
+Files: /usr/share/doc/jbrowse/html/*.html
diff --git a/debian/jbrowse.install b/debian/jbrowse.install
new file mode 100644
index 0000000..8677b62
--- /dev/null
+++ b/debian/jbrowse.install
@@ -0,0 +1,17 @@
+bin /var/www/jbrowse
+docs /var/www/jbrowse
+genome.css /var/www/jbrowse
+img /var/www/jbrowse
+index-debug.html /var/www/jbrowse
+index.html /var/www/jbrowse
+jar /var/www/jbrowse
+jbrowse.js /var/www/jbrowse
+js /var/www/jbrowse
+jslib /var/www/jbrowse
+lib /var/www/jbrowse
+openhand.cur /var/www/jbrowse
+release-notes.txt /var/www/jbrowse
+src /var/www/jbrowse
+tests /var/www/jbrowse
+touch.html /var/www/jbrowse
+twiki /var/www/jbrowse
diff --git a/debian/manpage.1.ex b/debian/manpage.1.ex
new file mode 100644
index 0000000..74ed50a
--- /dev/null
+++ b/debian/manpage.1.ex
@@ -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 JBROWSE SECTION "July 14, 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
+jbrowse \- program to do something
+.SH SYNOPSIS
+.B jbrowse
+.RI [ options ] " files" ...
+.br
+.B bar
+.RI [ options ] " files" ...
+.SH DESCRIPTION
+This manual page documents briefly the
+.B jbrowse
+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.
+\fBjbrowse\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
+jbrowse was written by <upstream author>.
+.PP
+This manual page was written by Steffen Moeller <moeller at debian.org>,
+for the Debian project (and may be used by others).
diff --git a/debian/manpage.sgml.ex b/debian/manpage.sgml.ex
new file mode 100644
index 0000000..8c0f5f5
--- /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>July 14, 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>moeller at debian.org</email>">
+ <!ENTITY dhusername "Steffen Moeller">
+ <!ENTITY dhucpackage "<refentrytitle>JBROWSE</refentrytitle>">
+ <!ENTITY dhpackage "jbrowse">
+
+ <!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..9ed4bed
--- /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 "Steffen Moeller">
+ <!ENTITY dhemail "moeller at debian.org">
+ <!-- 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 "jbrowse User Manual">
+ <!ENTITY dhucpackage "JBROWSE">
+ <!ENTITY dhpackage "jbrowse">
+]>
+
+<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>
+
diff --git a/debian/menu.ex b/debian/menu.ex
new file mode 100644
index 0000000..b290348
--- /dev/null
+++ b/debian/menu.ex
@@ -0,0 +1,2 @@
+?package(jbrowse):needs="X11|text|vc|wm" section="Applications/see-menu-manual"\
+ title="jbrowse" command="/usr/bin/jbrowse"
diff --git a/debian/patches/clean_patch.patch b/debian/patches/clean_patch.patch
new file mode 100644
index 0000000..daa4a2c
--- /dev/null
+++ b/debian/patches/clean_patch.patch
@@ -0,0 +1,13 @@
+Index: jbrowse-1.2.1/Makefile.in
+===================================================================
+--- jbrowse-1.2.1.orig/Makefile.in 2011-07-14 18:56:14.568535309 +0200
++++ jbrowse-1.2.1/Makefile.in 2011-07-14 18:56:21.752570902 +0200
+@@ -20,7 +20,7 @@
+ all: $(WIG2PNG_TARGET)
+
+ clean:
+- rm $(WIG2PNG_TARGET)
++ rm -f $(WIG2PNG_TARGET)
+
+ jbrowse: all
+ $(MAKE) -f $(TWIKI_PLUGIN_MAKEFILE) all
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..672cac8
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+clean_patch.patch
diff --git a/debian/postinst.ex b/debian/postinst.ex
new file mode 100644
index 0000000..be7d7da
--- /dev/null
+++ b/debian/postinst.ex
@@ -0,0 +1,39 @@
+#!/bin/sh
+# postinst script for jbrowse
+#
+# 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..ad60c0e
--- /dev/null
+++ b/debian/postrm.ex
@@ -0,0 +1,37 @@
+#!/bin/sh
+# postrm script for jbrowse
+#
+# 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..95763a1
--- /dev/null
+++ b/debian/preinst.ex
@@ -0,0 +1,35 @@
+#!/bin/sh
+# preinst script for jbrowse
+#
+# 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..f0ebcf0
--- /dev/null
+++ b/debian/prerm.ex
@@ -0,0 +1,38 @@
+#!/bin/sh
+# prerm script for jbrowse
+#
+# 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/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..552ba0c
--- /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 jbrowse-(.*)\.tar\.gz
+
+# Uncomment to examine a Webserver directory
+#http://www.example.com/pub/jbrowse-(.*)\.tar\.gz
+
+# Uncommment to examine a FTP server
+#ftp://ftp.example.com/pub/jbrowse-(.*)\.tar\.gz debian uupdate
+
+# Uncomment to find new files on sourceforge, for devscripts >= 2.9
+# http://sf.net/jbrowse/jbrowse-(.*)\.tar\.gz
+
+# Uncomment to find new files on GooglePages
+# http://example.googlepages.com/foo.html jbrowse-(.*)\.tar\.gz
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/jbrowse.git
More information about the debian-med-commit
mailing list