[med-svn] r2106 - in trunk/packages/emboss-explorer/trunk/debian: . patches
plessy at alioth.debian.org
plessy at alioth.debian.org
Sun Jun 29 14:36:32 UTC 2008
Author: plessy
Date: 2008-06-29 14:36:31 +0000 (Sun, 29 Jun 2008)
New Revision: 2106
Added:
trunk/packages/emboss-explorer/trunk/debian/apache.conf
trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.cron.daily
trunk/packages/emboss-explorer/trunk/debian/index.html
Removed:
trunk/packages/emboss-explorer/trunk/debian/acdcheck.1
trunk/packages/emboss-explorer/trunk/debian/acdcheck.xml
trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.cron.d
trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.dirs
trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.manpages
trunk/packages/emboss-explorer/trunk/debian/mkstatic.1
trunk/packages/emboss-explorer/trunk/debian/mkstatic.xml
trunk/packages/emboss-explorer/trunk/debian/patches/04-fix_install.dpatch
Modified:
trunk/packages/emboss-explorer/trunk/debian/README.Debian
trunk/packages/emboss-explorer/trunk/debian/changelog
trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.conf
trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.install
trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.links
trunk/packages/emboss-explorer/trunk/debian/patches/00list
trunk/packages/emboss-explorer/trunk/debian/patches/02-fix_Conf.pm.dpatch
trunk/packages/emboss-explorer/trunk/debian/rules
Log:
Moved the website to /usr/share/emboss-explorer. Use upstream's manpages.
* Package made compatible with FHS by not using /var/www.
- HTML files moved to `/usr/emboss-explorer/html'.
- Cascade stylesheets moved to `/etc/emboss-explorer/style'
(they are intended to be modifiable).
- Temporary files moved to `/var/lib/emboss-explorer'
- /etc/emboss-explorer/apache.conf allows apache2 to access the files in
the /user/share/emboss-explorer directory, as well as the EMBOSS
documentation in /usr/share/doc/emboss-explorer/ (Closes: #485735).
* debian/emboss-explorer.manpages, debian/acdcheck.1*, debian/mkstatic.1*
suppressed to use Upstream's manpages.
Modified: trunk/packages/emboss-explorer/trunk/debian/README.Debian
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/README.Debian 2008-06-29 11:54:29 UTC (rev 2105)
+++ trunk/packages/emboss-explorer/trunk/debian/README.Debian 2008-06-29 14:36:31 UTC (rev 2106)
@@ -1,23 +1,20 @@
emboss-explorer for Debian
--------------------------
-Visit http://localhost/cgi-bin/emboss to test EMBOSS.
-Site configuration (including a list of applications to be excluded from
-public access) is stored in the EMBOSS::GUI::Conf module (located at
-/usr/share/perl5/EMBOSS/GUI/Conf.pm).
+Visit http://localhost/emboss-explorer to test EMBOSS explorer. Site
+configuration (including a list of applications to be excluded from public
+access) is stored in /etc/emboss-explorer/emboss-explorer.conf).
-The main style sheet, which can be edited to customize the appearance of
-EMBOSS Explorer is /var/www/emboss-explorer/style/emboss.css. If you prefer the look and
-feel of the old EMBOSS GUI, you can use /var/www/emboss-explorer/style/classic.css
-instead (the style sheet is specified in the EMBOSS::GUI::Conf module).
+The main style sheet, which can be edited to customize the appearance of EMBOSS
+Explorer is `/etc/emboss-explorer/style/emboss.css'. If you prefer the look
+and feel of the old EMBOSS GUI, you can use `classic.css' instead (the style
+sheet is specified in /etc/emboss-explorer/emboss-explorer.conf).
EMBOSS Explorer generates temporary output files every time an application is
used. Depending on the tasks being performed, these output files can consume
-space fairly quickly. The old output can be cleaned up on a regular basis by
-adding a task to the root user's crontab. The following example runs every
-morning at 0400 and removes all output files that have not been accessed in
-the last 24 hours:
+space fairly quickly. The old output is cleaned up everyday at midnight by a
+task to the root user's crontab. By default, all output files that have not
+been accessed in the last 24 hours are removed. You can modify this in
+/etc/cron.daily/emboss-explorer.
-0 4 * * * find /var/www/emboss-explorer/output -type d -mindepth 1 -maxdepth 1 -atime 1 -exec rm -rf {} \;
-
- -- David Paleino <d.paleino at gmail.com> Sat, 12 May 2007 17:52:59 +0200
+ -- Charles Plessy <plessy at debian.org> Mon, 23 Jun 2008 22:43:36 +0900
Deleted: trunk/packages/emboss-explorer/trunk/debian/acdcheck.1
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/acdcheck.1 2008-06-29 11:54:29 UTC (rev 2105)
+++ trunk/packages/emboss-explorer/trunk/debian/acdcheck.1 2008-06-29 14:36:31 UTC (rev 2106)
@@ -1,48 +0,0 @@
-.\" Title: acdcheck
-.\" Author:
-.\" Generator: DocBook XSL Stylesheets v1.72.0 <http://docbook.sf.net/>
-.\" Date: may 12, 2007
-.\" Manual:
-.\" Source:
-.\"
-.TH "ACDCHECK" "1" "may 12, 2007" "" ""
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.SH "NAME"
-acdcheck \- parse EMBOSS ACD files
-.SH "SYNOPSIS"
-.HP 9
-\fBacdcheck\fR [\fB\-\-output\ \fR\fB\fIFORMAT\fR\fR] [\fBFILE\ \fR\fB\fI[\ FILE\ ...\ ]\fR\fR]
-.SH "DESCRIPTION"
-.PP
-This manual page documents briefly the
-\fBacdcheck\fR
-command.
-.PP
-\fBacdcheck\fR
-reads one or more named input FILEs and attempts to parse them as if they were EMBOSS ACD (AJAX Command Definition) files.
-.SH "OPTIONS"
-.PP
-\fB\-\-output \fR\fB\fIFORMAT\fR\fR
-.RS 4
-upon successful parsing of each ACD file, print a representation of the parse tree to standard output in the specified format. FORMAT must be one of either 'XML' or 'Perl' (case\-insensitive and without the quotes).
-.RE
-.SH "AUTHOR"
-.PP
-This manual page was written by David Paleino
-<d.paleino at gmail.com>
-for the
-Debian(TM)
-system (but 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.
-.PP
-On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common\-licenses/GPL.
-.PP
-emboss\-explorer, to which acdcheck belongs to, is (C) 2004, Luke McCarthy <mccarthy at users.sourceforge.net> emboss\-explorer is released under the Artistic license, which can be found, on Debian systems, in /usr/share/common\-licenses/Artistic.
-.SH "COPYRIGHT"
-Copyright \(co 2007 David Paleino
-.br
-
Deleted: trunk/packages/emboss-explorer/trunk/debian/acdcheck.xml
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/acdcheck.xml 2008-06-29 11:54:29 UTC (rev 2105)
+++ trunk/packages/emboss-explorer/trunk/debian/acdcheck.xml 2008-06-29 14:36:31 UTC (rev 2106)
@@ -1,127 +0,0 @@
-<?xml version='1.0' encoding='ISO-8859-1'?>
-<?xml-stylesheet type="text/xsl"
- href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
-<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.2//EN"
-"http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd" [
-
-<!--
-
-Process this file with an XSLT processor: `xsltproc \
--''-nonet /usr/share/sgml/docbook/stylesheet/xsl/nwalsh/\
-manpages/docbook.xsl manpage.dbk'. 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
-
-manpage.1: manpage.dbk
- $(XP) $(DB2MAN) $<
-
-The xsltproc binary is found in the xsltproc package. The
-XSL files are in docbook-xsl. 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.
-
--->
-
- <!-- Fill in your name for FIRSTNAME and SURNAME. -->
- <!ENTITY dhfirstname "<firstname>David</firstname>">
- <!ENTITY dhsurname "<surname>Paleino</surname>">
- <!-- Please adjust the date whenever revising the manpage. -->
- <!ENTITY dhdate "<date>may 12, 2007</date>">
- <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
- allowed: see man(7), man(1). -->
- <!ENTITY dhsection "<manvolnum>1</manvolnum>">
- <!ENTITY dhemail "<email>d.paleino at gmail.com</email>">
- <!ENTITY dhusername "David Paleino">
- <!ENTITY dhucpackage "<refentrytitle>acdcheck</refentrytitle>">
- <!ENTITY dhpackage "acdcheck">
-
- <!ENTITY debian "<productname>Debian</productname>">
- <!ENTITY gnu "<acronym>GNU</acronym>">
- <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
-]>
-
-<refentry>
- <refentryinfo>
- <address>
- &dhemail;
- </address>
- <copyright>
- <year>2007</year>
- <holder>&dhusername;</holder>
- </copyright>
- &dhdate;
- </refentryinfo>
- <refmeta>
- &dhucpackage;
-
- &dhsection;
- </refmeta>
- <refnamediv>
- <refname>&dhpackage;</refname>
-
- <refpurpose>parse EMBOSS ACD files</refpurpose>
- </refnamediv>
- <refsynopsisdiv>
- <cmdsynopsis>
- <command>&dhpackage;</command>
-
- <arg><option>--output <replaceable>FORMAT</replaceable></option></arg>
-
- <arg><option>FILE <replaceable>[ FILE ... ]</replaceable></option></arg>
- </cmdsynopsis>
- </refsynopsisdiv>
- <refsect1>
- <title>DESCRIPTION</title>
-
- <para>This manual page documents briefly the
- <command>&dhpackage;</command> command.</para>
-
- <para><command>&dhpackage;</command> reads one or more named
- input FILEs and attempts to parse them as if they were
- EMBOSS ACD (AJAX Command Definition) files.</para>
-
- </refsect1>
- <refsect1>
- <title>OPTIONS</title>
-
- <variablelist>
- <varlistentry>
- <term><option>--output <replaceable>FORMAT</replaceable></option></term>
- <listitem>
- <para>
- upon successful parsing of each ACD file, print a representation of the
- parse tree to standard output in the specified format. FORMAT must be
- one of either 'XML' or 'Perl' (case-insensitive and without the quotes).
- </para>
- </listitem>
- </varlistentry>
- </variablelist>
- </refsect1>
- <refsect1>
- <title>AUTHOR</title>
-
- <para>This manual page was written by &dhusername; &dhemail; for
- the &debian; system (but 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>
- <para>
- emboss-explorer, to which &dhpackage; belongs to, is
- (C) 2004, Luke McCarthy <mccarthy at users.sourceforge.net>
-
- emboss-explorer is released under the Artistic license, which
- can be found, on Debian systems, in /usr/share/common-licenses/Artistic.
- </para>
- </refsect1>
-</refentry>
Added: trunk/packages/emboss-explorer/trunk/debian/apache.conf
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/apache.conf (rev 0)
+++ trunk/packages/emboss-explorer/trunk/debian/apache.conf 2008-06-29 14:36:31 UTC (rev 2106)
@@ -0,0 +1,22 @@
+# I used /etc/gallery2/apache.conf as a template. -- Charles Plessy
+Alias /emboss-explorer /usr/share/emboss-explorer/html
+
+<Directory /usr/share/emboss-explorer/html>
+ Options FollowSymLinks
+# AllowOverride Limit Options FileInfo
+</Directory>
+
+Alias /doc/emboss-explorer/ "/usr/share/doc/emboss-explorer/"
+<Directory "/usr/share/doc/emboss-explorer/">
+ Options Indexes MultiViews FollowSymLinks
+ AllowOverride None
+ Order allow,deny
+ Allow from all
+</Directory>
+
+# some people prefer a simple URL like http://emboss-explorer.example
+#<VirtualHost 1.2.3.4>
+# DocumentRoot /usr/share/emboss-explorer
+# ServerName emboss-explorer.example
+#</VirtualHost>
+
Modified: trunk/packages/emboss-explorer/trunk/debian/changelog
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/changelog 2008-06-29 11:54:29 UTC (rev 2105)
+++ trunk/packages/emboss-explorer/trunk/debian/changelog 2008-06-29 14:36:31 UTC (rev 2106)
@@ -1,15 +1,27 @@
-emboss-explorer (2.2.0-6) UNRELEASED; urgency=medium
+emboss-explorer (2.2.0-6) UNRELEASED; urgency=low
-BROKEN: work in progress, and I do not know why debian/rules install tries to
-put things in /usr/local...
-
[ Charles Plessy ]
* Relicensed the packaging work to "Same as EMBOSS explorer".
- * Documented the patches, and forwarded the that moves
- the configuration to `/etc/emboss-explorer.conf'.
+ * debian/patches:
+ - Documented 01-fix_examples.dpatch.
+ - Documented and forwarded 02-fix_Conf.pm.dpatch and
+ 05-build-manpages.dpatch.
+ - Suppressed 04-fix_install.dpatch. Its role is taken by debian/rules and
+ debian/index.html.
* debian/rules:
- refreshed using dh-make-perl version 0.45;
- - tests disable because of upstream bug 1994385.
+ - tests disable because of upstream bug 1994385;
+ - sets the owner of the emboss output directory as `www-data'.
+ * Package made compatible with FHS by not using /var/www.
+ - HTML files moved to `/usr/emboss-explorer/html'.
+ - Cascade stylesheets moved to `/etc/emboss-explorer/style'
+ (they are intended to be modifiable).
+ - Temporary files moved to `/var/lib/emboss-explorer'
+ - /etc/emboss-explorer/apache.conf allows apache2 to access the files in
+ the /user/share/emboss-explorer directory, as well as the EMBOSS
+ documentation in /usr/share/doc/emboss-explorer/ (Closes: #485735).
+ * debian/emboss-explorer.manpages, debian/acdcheck.1*, debian/mkstatic.1*
+ suppressed to use Upstream's manpages.
[ David Paleino ]
* debian/control:
@@ -18,7 +30,7 @@
- updated Charles' email :)
* debian/copyright updated
- -- David Paleino <d.paleino at gmail.com> Wed, 11 Jun 2008 10:03:39 +0200
+ -- Charles Plessy <plessy at debian.org> Mon, 23 Jun 2008 22:43:45 +0900
emboss-explorer (2.2.0-5) unstable; urgency=low
Modified: trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.conf
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.conf 2008-06-29 11:54:29 UTC (rev 2105)
+++ trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.conf 2008-06-29 14:36:31 UTC (rev 2106)
@@ -1,5 +1,5 @@
# path to the EMBOSS::GUI HTML files
-our $HTML_PATH = "/var/www/emboss-explorer";
+our $HTML_PATH = "/usr/share/emboss-explorer/html";
# URL corresponding to $HTML_PATH above
our $HTML_URL = "/emboss-explorer";
@@ -8,13 +8,13 @@
our $STYLE_URL = "$HTML_URL/style/emboss.css";
# URL prefix to place before image links
-our $IMAGE_URL = "/images/emboss-explorer";
+our $IMAGE_URL = "$EMBOSS_HOME/doc/html/";
# URL prefix to place before manual links (only used in static pages)
our $MANUAL_URL = "/doc/emboss-explorer/html";
# path to the EMBOSS::GUI temporary output directory
-our $OUTPUT_PATH = "/var/www/emboss-explorer/output";
+our $OUTPUT_PATH = "/var/lib/emboss-explorer/output";
# URL corresponding to $OUTPUT_PATH above
our $OUTPUT_URL = "/emboss-explorer/output";
Deleted: trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.cron.d
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.cron.d 2008-06-29 11:54:29 UTC (rev 2105)
+++ trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.cron.d 2008-06-29 14:36:31 UTC (rev 2106)
@@ -1 +0,0 @@
-0 0 * * * root [ -d "/var/www/emboss-explorer/output" ] && find /var/www/emboss-explorer/output -mindepth 1 -maxdepth 1 -atime 1 -exec rm -rf {} \;
Copied: trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.cron.daily (from rev 2087, trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.cron.d)
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.cron.daily (rev 0)
+++ trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.cron.daily 2008-06-29 14:36:31 UTC (rev 2106)
@@ -0,0 +1,6 @@
+#!/bin/sh
+
+# Daily cleaning task for EMBOSS explorer.
+# Modifications to this files are preserved during upgrades.
+
+[ -d "/var/lib/emboss-explorer/output" ] && find /var/lib/emboss-explorer/output -mindepth 1 -maxdepth 1 -atime 1 -exec rm -rf {} \;
Deleted: trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.dirs
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.dirs 2008-06-29 11:54:29 UTC (rev 2105)
+++ trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.dirs 2008-06-29 14:36:31 UTC (rev 2106)
@@ -1,6 +0,0 @@
-usr/bin
-usr/lib/cgi-bin
-usr/share/images/emboss-explorer
-usr/share/emboss-explorer
-var/www/emboss-explorer/output
-var/www/emboss-explorer/style
Modified: trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.install
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.install 2008-06-29 11:54:29 UTC (rev 2105)
+++ trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.install 2008-06-29 14:36:31 UTC (rev 2106)
@@ -1,6 +1,6 @@
-html/index.html var/www/emboss-explorer/
-html/images/* usr/share/images/emboss-explorer/
-html/style/* var/www/emboss-explorer/style/
/cgi/emboss usr/lib/cgi-bin/
-/bin/* usr/bin/
-debian/emboss-explorer.conf etc/
+html/style/* etc/emboss-explorer/style/
+debian/emboss-explorer.conf etc/emboss-explorer/
+debian/apache.conf etc/emboss-explorer/
+debian/index.html usr/share/emboss-explorer/html
+html/images/* usr/share/emboss-explorer/images
Modified: trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.links
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.links 2008-06-29 11:54:29 UTC (rev 2105)
+++ trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.links 2008-06-29 14:36:31 UTC (rev 2106)
@@ -1 +1,4 @@
usr/share/EMBOSS/doc/html/emboss/apps/ usr/share/doc/emboss-explorer/html
+etc/emboss-explorer/apache.conf etc/apache2/conf.d/emboss-explorer
+etc/emboss-explorer/style/ usr/share/emboss-explorer/html/style
+var/lib/emboss-explorer/output usr/share/emboss-explorer/html/output
Deleted: trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.manpages
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.manpages 2008-06-29 11:54:29 UTC (rev 2105)
+++ trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.manpages 2008-06-29 14:36:31 UTC (rev 2106)
@@ -1,2 +0,0 @@
-debian/acdcheck.1
-debian/mkstatic.1
Added: trunk/packages/emboss-explorer/trunk/debian/index.html
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/index.html (rev 0)
+++ trunk/packages/emboss-explorer/trunk/debian/index.html 2008-06-29 14:36:31 UTC (rev 2106)
@@ -0,0 +1,11 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Frameset//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-frameset.dtd">
+<html xmlns='http://www.w3.org/1999/xhtml' xml:lang='en' lang='en'>
+ <head>
+ <title>EMBOSS Explorer</title>
+ </head>
+ <frameset cols="170, *">
+ <frame src="/cgi-bin/emboss/menu" name="menu" />
+ <frame src="/cgi-bin/emboss/intro" name="main" />
+ </frameset>
+</html>
Property changes on: trunk/packages/emboss-explorer/trunk/debian/index.html
___________________________________________________________________
Name: svn:executable
+ *
Deleted: trunk/packages/emboss-explorer/trunk/debian/mkstatic.1
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/mkstatic.1 2008-06-29 11:54:29 UTC (rev 2105)
+++ trunk/packages/emboss-explorer/trunk/debian/mkstatic.1 2008-06-29 14:36:31 UTC (rev 2106)
@@ -1,53 +0,0 @@
-.\" Title: mkstatic
-.\" Author:
-.\" Generator: DocBook XSL Stylesheets v1.72.0 <http://docbook.sf.net/>
-.\" Date: may 12, 2007
-.\" Manual:
-.\" Source:
-.\"
-.TH "MKSTATIC" "1" "may 12, 2007" "" ""
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.SH "NAME"
-mkstatic \- print static EMBOSS\-Explorer pages
-.SH "SYNOPSIS"
-.HP 9
-\fBmkstatic\fR [\fB\-\-frames\ |\ \-\-noframes\fR] [\fB\-\-cgi\ \fR\fB\fIURL\fR\fR] [\fB\fIDIRECTORY\fR\fR]
-.SH "DESCRIPTION"
-.PP
-This manual page documents briefly the
-\fBmkstatic\fR
-command.
-.PP
-\fBmkstatic\fR
-prints EMBOSS\-Explorer pages in a static way, so that you don't need to run any cgi script.
-.SH "OPTIONS"
-.PP
-\fB\-\-frames | \-\-noframes\fR
-.RS 4
-controls whether or not the generated HTML has a separate frame for the application menu. The default is to use a separate frame.
-.RE
-.PP
-\fB\-\-cgi \fR\fB\fIURL\fR\fR
-.RS 4
-use the specified URL as the location of the CGI script that application input forms are submitted to.
-.RE
-.SH "AUTHOR"
-.PP
-This manual page was written by David Paleino
-<d.paleino at gmail.com>
-for the
-Debian(TM)
-system (but 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.
-.PP
-On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common\-licenses/GPL.
-.PP
-emboss\-explorer, to which mkstatic belongs to, is (C) 2004, Luke McCarthy <mccarthy at users.sourceforge.net> emboss\-explorer is released under the Artistic license, which can be found, on Debian systems, in /usr/share/common\-licenses/Artistic.
-.SH "COPYRIGHT"
-Copyright \(co 2007 David Paleino
-.br
-
Deleted: trunk/packages/emboss-explorer/trunk/debian/mkstatic.xml
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/mkstatic.xml 2008-06-29 11:54:29 UTC (rev 2105)
+++ trunk/packages/emboss-explorer/trunk/debian/mkstatic.xml 2008-06-29 14:36:31 UTC (rev 2106)
@@ -1,132 +0,0 @@
-<?xml version='1.0' encoding='ISO-8859-1'?>
-<?xml-stylesheet type="text/xsl"
- href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
-<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.2//EN"
-"http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd" [
-
-<!--
-
-Process this file with an XSLT processor: `xsltproc \
--''-nonet /usr/share/sgml/docbook/stylesheet/xsl/nwalsh/\
-manpages/docbook.xsl manpage.dbk'. 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
-
-manpage.1: manpage.dbk
- $(XP) $(DB2MAN) $<
-
-The xsltproc binary is found in the xsltproc package. The
-XSL files are in docbook-xsl. 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.
-
--->
-
- <!-- Fill in your name for FIRSTNAME and SURNAME. -->
- <!ENTITY dhfirstname "<firstname>David</firstname>">
- <!ENTITY dhsurname "<surname>Paleino</surname>">
- <!-- Please adjust the date whenever revising the manpage. -->
- <!ENTITY dhdate "<date>may 12, 2007</date>">
- <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
- allowed: see man(7), man(1). -->
- <!ENTITY dhsection "<manvolnum>1</manvolnum>">
- <!ENTITY dhemail "<email>d.paleino at gmail.com</email>">
- <!ENTITY dhusername "David Paleino">
- <!ENTITY dhucpackage "<refentrytitle>mkstatic</refentrytitle>">
- <!ENTITY dhpackage "mkstatic">
-
- <!ENTITY debian "<productname>Debian</productname>">
- <!ENTITY gnu "<acronym>GNU</acronym>">
- <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
-]>
-
-<refentry>
- <refentryinfo>
- <address>
- &dhemail;
- </address>
- <copyright>
- <year>2007</year>
- <holder>&dhusername;</holder>
- </copyright>
- &dhdate;
- </refentryinfo>
- <refmeta>
- &dhucpackage;
-
- &dhsection;
- </refmeta>
- <refnamediv>
- <refname>&dhpackage;</refname>
-
- <refpurpose>print static EMBOSS-Explorer pages</refpurpose>
- </refnamediv>
- <refsynopsisdiv>
- <cmdsynopsis>
- <command>&dhpackage;</command>
-
- <arg><option>--frames | --noframes</option></arg>
- <arg><option>--cgi <replaceable>URL</replaceable></option></arg>
- <arg><option><replaceable>DIRECTORY</replaceable></option></arg>
-
- </cmdsynopsis>
- </refsynopsisdiv>
- <refsect1>
- <title>DESCRIPTION</title>
-
- <para>This manual page documents briefly the
- <command>&dhpackage;</command> command.</para>
-
- <para><command>&dhpackage;</command> prints EMBOSS-Explorer pages in
- a static way, so that you don't need to run any cgi script.</para>
-
- </refsect1>
- <refsect1>
- <title>OPTIONS</title>
-
- <variablelist>
- <varlistentry>
- <term><option>--frames | --noframes</option></term>
- <listitem>
- <para>
- controls whether or not the generated HTML has a separate frame for the
- application menu. The default is to use a separate frame.</para>
- </listitem>
- </varlistentry>
- <varlistentry>
- <term><option>--cgi <replaceable>URL</replaceable></option></term>
- <listitem>
- <para>use the specified URL as the location of the CGI script that
- application input forms are submitted to.</para>
- </listitem>
- </varlistentry>
- </variablelist>
- </refsect1>
- <refsect1>
- <title>AUTHOR</title>
-
- <para>This manual page was written by &dhusername; &dhemail; for
- the &debian; system (but 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>
- <para>
- emboss-explorer, to which &dhpackage; belongs to, is
- (C) 2004, Luke McCarthy <mccarthy at users.sourceforge.net>
-
- emboss-explorer is released under the Artistic license, which
- can be found, on Debian systems, in /usr/share/common-licenses/Artistic.
- </para>
- </refsect1>
-</refentry>
Modified: trunk/packages/emboss-explorer/trunk/debian/patches/00list
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/patches/00list 2008-06-29 11:54:29 UTC (rev 2105)
+++ trunk/packages/emboss-explorer/trunk/debian/patches/00list 2008-06-29 14:36:31 UTC (rev 2106)
@@ -1,4 +1,3 @@
01-fix_examples.dpatch
02-fix_Conf.pm.dpatch
-04-fix_install.dpatch
05-build-manpages.dpatch
Modified: trunk/packages/emboss-explorer/trunk/debian/patches/02-fix_Conf.pm.dpatch
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/patches/02-fix_Conf.pm.dpatch 2008-06-29 11:54:29 UTC (rev 2105)
+++ trunk/packages/emboss-explorer/trunk/debian/patches/02-fix_Conf.pm.dpatch 2008-06-29 14:36:31 UTC (rev 2106)
@@ -86,7 +86,7 @@
-
-# whether or not to display using frames
-our $FRAMES = 1;
-+open (config_file, "</etc/emboss-explorer.conf") or die "Cannot load /etc/emboss-explorer.conf!";
++open (config_file, "</etc/emboss-explorer/emboss-explorer.conf") or die "Cannot load /etc/emboss-explorer.conf!";
+my @conf = <config_file>;
+eval join("\n", @conf);
+die $@ if $@;
Deleted: trunk/packages/emboss-explorer/trunk/debian/patches/04-fix_install.dpatch
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/patches/04-fix_install.dpatch 2008-06-29 11:54:29 UTC (rev 2105)
+++ trunk/packages/emboss-explorer/trunk/debian/patches/04-fix_install.dpatch 2008-06-29 14:36:31 UTC (rev 2106)
@@ -1,145 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 01-fix_install.dpatch by David Paleino <d.paleino at gmail.com>
-##
-## All lines beginning with `## DP:' are a description of the patch.
-## DP: Set install script with default values plus some other
-## DP: hack.
-## DP: Forwarded: No. This patch has to be reviewed to see if it can
-## DP: be replaced by another workaround.
-
- at DPATCH@
---- ./install 2007-07-04 21:07:32.000000000 +0900
-+++ ./install.dp 2007-07-04 21:12:36.000000000 +0900
-@@ -1,68 +1,8 @@
- #!/bin/sh
-+BUILD_DIR=./debian/emboss-explorer
-
--usage() {
-- cat <<EOF
--this script must be executed from the top-level directory of the
--EMBOSS Explorer distribution.
--EOF
-- exit 1
--}
-+HTML_PATH=/var/www/emboss-explorer
-
--prompt() {
-- echo -e "$1\n\t(default is $2)"
-- read INPUT
-- eval $3=${INPUT:-$2}
--}
--
--echo installing EMBOSS Explorer perl modules...
--echo
--perl Makefile.PL && make && make install || exit
--
--echo installing EMBOSS Explorer GUI components...
--echo
--echo I need to collect some information in order to install EMBOSS Explorer:
--
--EMBOSS_PREFIX=`embossversion -full 2>/dev/null | awk '/^InstallDirectory/ { print $2 }'`
--prompt "Where was EMBOSS installed?" ${EMBOSS_PREFIX:-/usr/local} EMBOSS_PREFIX
--
--# TODO something fancy to guess the web root?
--prompt "Where should the EMBOSS Explorer HTML files be installed?" /var/www/html/emboss HTML_PATH
--OUTPUT_PATH=$HTML_PATH/output
--
--prompt "What is the URL prefix corresponding to the HTML directory above?" /emboss HTML_URL
--OUTPUT_URL=$HTML_URL/output
--
--prompt "Where should the EMBOSS Explorer CGI script be installed?" /var/www/cgi-bin/emboss CGI_PATH
--
--if [ -d $CGI_PATH ]
--then
-- CGI_DIR=$CGI_PATH
-- CGI_PATH=$CGI_DIR/emboss
--else
-- CGI_DIR=${CGI_PATH%/*}
--fi
--
--prompt "What is the complete URL corresponding to the CGI script '$CGI_PATH'?" /cgi-bin/emboss CGI_URL
--
--# munge EMBOSS::GUI::Conf according to the information above...
--CONF_MODULE=`perl -MEMBOSS::GUI::Conf -e 'print $INC{"EMBOSS/GUI/Conf.pm"}'`
--perl -pi -e "
-- \$HTML_PATH = '$HTML_PATH'; s/(?<=HTML_PATH = \")[^\"]*/\$HTML_PATH/;
-- \$HTML_URL='$HTML_URL'; s/(?<=HTML_URL = \")[^\"]*/\$HTML_URL/;
-- \$OUTPUT_PATH = '$OUTPUT_PATH'; s/(?<=OUTPUT_PATH = \")[^\"]*/\$OUTPUT_PATH/;
-- \$OUTPUT_URL='$OUTPUT_URL'; s/(?<=OUTPUT_URL = \")[^\"]*/\$OUTPUT_URL/;
-- \$EMBOSS_PREFIX='$EMBOSS_PREFIX'; s/(?<=EMBOSS_PREFIX = \")[^\"]*/\$EMBOSS_PREFIX/;
--" $CONF_MODULE
--
--# install HTML and CGI files...
--[ -d html ] || usage
--echo installing HTML files to $HTML_PATH...
--if [ -d $HTML_PATH ]
--then
-- cp -rp html/* $HTML_PATH
--else
-- cp -rp html $HTML_PATH
--fi
- echo creating HTML index file at $HTML_PATH/index.html...
- echo "<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Frameset//EN\"
- \"http://www.w3.org/TR/xhtml1/DTD/xhtml1-frameset.dtd\">
-@@ -71,58 +11,7 @@
- <title>EMBOSS Explorer</title>
- </head>
- <frameset cols=\"170, *\">
-- <frame src=\"$CGI_URL/menu\" name=\"menu\" />
-- <frame src=\"$CGI_URL/intro\" name=\"main\" />
-+ <frame src=\"/cgi-bin/emboss/menu\" name=\"menu\" />
-+ <frame src=\"/cgi-bin/emboss/intro\" name=\"main\" />
- </frameset>
--</html>" >$HTML_PATH/index.html
--echo creating output directory at $OUTPUT_PATH...
--[ -d $OUTPUT_PATH ] || mkdir $OUTPUT_PATH
--#echo creating .htaccess file in $OUTPUT_PATH/.htaccess...
--#echo "Header add Cache-Control: no-cache" >>$OUTPUT_PATH/.htaccess
--echo installing CGI script to $CGI_PATH...
--cp cgi/emboss $CGI_PATH
--
--# copy support files used in the program manuals...
--echo copying manual support files to $HTML_PATH/manual...
--[ -d $HTML_PATH/manual ] || mkdir $HTML_PATH/manual
--# EMBOSS 3
--find $EMBOSS_PREFIX/share/EMBOSS/doc/programs/html -type f ! -name '*.html' -exec cp {} $HTML_PATH/manual \;
--# EMBOSS 4
--find $EMBOSS_PREFIX/share/EMBOSS/doc/html/emboss/apps -type f ! -name '*.html' -exec cp {} $HTML_PATH/manual \;
--
--# fix permissions...
--echo fixing permissions...
--find $HTML_PATH -type d -exec chmod a+rx {} \; -o -type f -exec chmod a+r {} \;
--chmod a+rwx $OUTPUT_PATH
--chmod a+rx $CGI_PATH
--
--# TODO mention cron script in bin directory, when it exists...
--CRON="0 4 * * * find $OUTPUT_PATH -type d -mindepth 1 -maxdepth 1 -atime 1 -exec rm -rf {} \;"
--
--# mention location of configuration file and things that can be changed (list
--# of excluded applications, mostly...)
--
--cat <<EOF
--
--EMBOSS Explorer is installed. Visit $CGI_URL to test it out.
--Site configuration (including a list of applications to be excluded from
--public access) is stored in the EMBOSS::GUI::Conf module (located at $CONF_MODULE).
--
--The main style sheet, which can be edited to customize the appearance of
--EMBOSS Explorer is $HTML_PATH/style/emboss.css. If you prefer the look and
--feel of the old EMBOSS GUI, you can use $HTML_PATH/style/classic.css
--instead (the style sheet is specified in the EMBOSS::GUI::Conf module).
--
--EMBOSS Explorer generates temporary output files every time an application is
--used. Depending on the tasks being performed, these output files can consume
--space fairly quickly. The old output can be cleaned up on a regular basis by
--adding a task to the root user's crontab. The following example runs every
--morning at 0400 and removes all output files that have not been accessed in
--the last 24 hours:
--
--0 4 * * * find $OUTPUT_PATH -type d -mindepth 1 -maxdepth 1 -atime 1 -exec rm -rf {} \;
--
--Please report any errors or strange occurrences using the bug tracker at
--http://sourceforge.net/tracker/?func=add&group_id=124389&atid=699414
--
--EOF
-+</html>" >$BUILD_DIR$HTML_PATH/index.html
Modified: trunk/packages/emboss-explorer/trunk/debian/rules
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/rules 2008-06-29 11:54:29 UTC (rev 2105)
+++ trunk/packages/emboss-explorer/trunk/debian/rules 2008-06-29 14:36:31 UTC (rev 2106)
@@ -5,14 +5,15 @@
# be used freely wherever it is useful.
# Uncomment this to turn on verbose mode.
-export DH_VERBOSE=1
+# export DH_VERBOSE=1
# If set to a true value then MakeMaker's prompt function will
# always return the default without waiting for user input.
export PERL_MM_USE_DEFAULT=1
PERL ?= /usr/bin/perl
-PACKAGE = emboss-explorer # was: $(shell dh_listpackages)
+# was: $(shell dh_listpackages)
+PACKAGE = emboss-explorer
TMP = $(CURDIR)/debian/$(PACKAGE)
include /usr/share/dpatch/dpatch.make
@@ -40,12 +41,14 @@
dh_clean -k
# Add commands to install the package into $(TMP) here
$(MAKE) install DESTDIR=$(TMP) PREFIX=/usr
- ./install
[ ! -d $(TMP)/usr/lib/perl5 ] || \
rmdir --ignore-fail-on-non-empty --parents --verbose \
$(TMP)/usr/lib/perl5
- chown -R www-data $(CURDIR)/debian/emboss-explorer/var/www/emboss-explorer/output
- # ACD.pm desserves its own package.
+ dh_installdirs var/lib/emboss-explorer/output
+ chown -R www-data $(CURDIR)/debian/emboss-explorer/var/lib/emboss-explorer/output
+ # Move ACD.pm to a separate package, that is useful for making
+ # manpages from EMBOSS ACD files without being bothered by the
+ # dependancy on web servers.
mv $(CURDIR)/debian/emboss-explorer/usr/share/perl5/EMBOSS/ACD.pm $(CURDIR)/debian/libemboss-acd-perl/usr/share/perl5/EMBOSS/
mv $(CURDIR)/debian/emboss-explorer/usr/share/man/man3/EMBOSS::ACD.3pm $(CURDIR)/debian/libemboss-acd-perl/usr/share/man/man3/
touch $@
@@ -65,6 +68,7 @@
dh_perl
dh_compress
dh_fixperms
+ chown -R www-data $(CURDIR)/debian/emboss-explorer/var/lib/emboss-explorer/output
dh_installdeb
dh_gencontrol
dh_md5sums
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