[med-svn] r2012 - in trunk/packages/emboss-explorer/trunk/debian: . patches

Wed Jun 11 07:32:32 UTC 2008

Author: hanska-guest
Date: 2008-06-11 07:32:31 +0000 (Wed, 11 Jun 2008)
New Revision: 2012

Added:
   trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.conf
Removed:
   trunk/packages/emboss-explorer/trunk/debian/patches/03-add_conffile.dpatch
Modified:
   trunk/packages/emboss-explorer/trunk/debian/README.Debian
   trunk/packages/emboss-explorer/trunk/debian/changelog
   trunk/packages/emboss-explorer/trunk/debian/control
   trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.cron.d
   trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.install
   trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.postinst
   trunk/packages/emboss-explorer/trunk/debian/patches/00list
   trunk/packages/emboss-explorer/trunk/debian/patches/04-fix_install.dpatch
   trunk/packages/emboss-explorer/trunk/debian/rules
Log:
Using /usr/lib/emboss instead of /usr/bin, and /var/www/emboss-explorer instead of /var/www/emboss. Other minor changes to simplify build system.
Date: 2007-07-04 15:00:59

Modified: trunk/packages/emboss-explorer/trunk/debian/README.Debian
===================================================================

--- trunk/packages/emboss-explorer/trunk/debian/README.Debian	2008-06-11 07:31:13 UTC (rev 2011)
+++ trunk/packages/emboss-explorer/trunk/debian/README.Debian	2008-06-11 07:32:31 UTC (rev 2012)
@@ -7,8 +7,8 @@
 /usr/share/perl5/EMBOSS/GUI/Conf.pm).
 
 The main style sheet, which can be edited to customize the appearance of
-EMBOSS Explorer is /var/www/emboss/style/emboss.css.  If you prefer the look and
-feel of the old EMBOSS GUI, you can use /var/www/emboss/style/classic.css
+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).
 
 EMBOSS Explorer generates temporary output files every time an application is
@@ -18,6 +18,6 @@
 morning at 0400 and removes all output files that have not been accessed in
 the last 24 hours:
 
-0 4 * * * find /var/www/emboss/output -type d -mindepth 1 -maxdepth 1 -atime 1 -exec rm -rf {} \;
+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

Modified: trunk/packages/emboss-explorer/trunk/debian/changelog
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/changelog	2008-06-11 07:31:13 UTC (rev 2011)
+++ trunk/packages/emboss-explorer/trunk/debian/changelog	2008-06-11 07:32:31 UTC (rev 2012)
@@ -1,3 +1,20 @@
+emboss-explorer (2.2.0-2) unstable; urgency=low
+
+  * Migration from /var/www/emboss to /var/www/emboss-explorer was
+    incomplete. Correcting this.
+  * Fixed double-building of the manpages.
+  * Added myself to the uploaders.
+  * Swiched to apache2 as the default webserver.
+  * emboss-explorer.conf now defaults to /var/lib/emboss, which is the
+    only place where the emboss binaries are guaranteed to keep their
+    original name.
+  * Provides emboss-explorer.conf through a file, not a patch. Modifying
+    ./install so that ti does not manipulate emboss-explorer.conf anymore.
+  * Added a configure rule so that the clean rule can always run make clean.
+  * Using include /usr/share/dpatch/dpatch.make.
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org>  Wed,  4 Jul 2007 21:46:03 +0900
+
 emboss-explorer (2.2.0-1) experimental; urgency=low
 
   * Initial release (Closes: #423548)

Modified: trunk/packages/emboss-explorer/trunk/debian/control
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/control	2008-06-11 07:31:13 UTC (rev 2011)
+++ trunk/packages/emboss-explorer/trunk/debian/control	2008-06-11 07:32:31 UTC (rev 2012)
@@ -2,7 +2,7 @@
 Section: science
 Priority: optional
 Maintainer: Debian EMBOSS Packaging Team <pkg-emboss-devel at lists.alioth.debian.org>
-Uploaders: David Paleino <d.paleino at gmail.com>
+Uploaders: David Paleino <d.paleino at gmail.com>, Charles Plessy <charles-debian-nospam at plessy.org>
 Build-Depends: debhelper (>= 5)
 Build-Depends-Indep: xsltproc, docbook-xsl, docbook-xml, libparse-recdescent-perl, dpatch, libmailtools-perl
 Standards-Version: 3.7.2
@@ -11,7 +11,7 @@
 
 Package: emboss-explorer
 Architecture: all
-Depends: ${misc:Depends}, ${perl:Depends}, libmailtools-perl, emboss, libemboss-acd-perl, emboss-data, apache | apache2 | httpd-cgi
+Depends: ${misc:Depends}, ${perl:Depends}, libmailtools-perl, emboss, libemboss-acd-perl, emboss-data, apache2 | httpd-cgi
 Recommends: emboss-doc
 Description: web-based GUI to EMBOSS
  EMBOSS explorer is a web-based graphical user interface

Added: trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.conf
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.conf	                        (rev 0)
+++ trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.conf	2008-06-11 07:32:31 UTC (rev 2012)
@@ -0,0 +1,66 @@
+# path to the EMBOSS::GUI HTML files
+our $HTML_PATH = "/var/www/emboss-explorer";
+
+# URL corresponding to $HTML_PATH above
+our $HTML_URL = "/emboss-explorer";
+
+# URL specifying the style sheet to use
+our $STYLE_URL = "$HTML_URL/style/emboss.css";
+
+# URL prefix to place before image links
+our $IMAGE_URL = "/images/emboss-explorer";
+
+# 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";
+
+# URL corresponding to $OUTPUT_PATH above
+our $OUTPUT_URL = "/emboss-explorer/output";
+
+# prefix under which EMBOSS was installed
+our $EMBOSS_PREFIX = "/usr";
+
+# path to EMBOSS binaries
+our $EMBOSS_BIN = "/var/lib/emboss";
+
+# path to EMBOSS installation
+our $EMBOSS_HOME = "$EMBOSS_PREFIX/share/EMBOSS";
+
+# path to EMBOSS ACD files
+our $EMBOSS_ACDROOT = "$EMBOSS_HOME/acd";
+
+# path to EMBOSS data
+our $EMBOSS_DATA = "$EMBOSS_HOME/data";
+
+# path to EMBOSS application manuals
+our $EMBOSS_MANUAL = "$EMBOSS_HOME/doc/html";
+
+# list of groups and applications to exclude from the main menu
+our @EXCLUDED = (
+	"ACD",
+	"acdc",
+	"acdpretty",
+	"acdtable",
+	"acdtrace",
+	"acdvalid",
+	"UTILS DATABASE CREATION",
+	"aaindexextract",
+	"cutgextract",
+	"printsextract",
+	"prosextract",
+	"rebaseextract",
+	"tfextract",
+	"UTILS DATABASE INDEXING",
+	"dbiblast",
+	"dbifasta",
+	"dbiflat",
+	"dbigcg",
+);
+
+# number of seconds to delay between placeholder page refreshes
+our $REFRESH_DELAY = 1;
+
+# whether or not to display using frames
+our $FRAMES = 1;

Modified: trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.cron.d
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.cron.d	2008-06-11 07:31:13 UTC (rev 2011)
+++ trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.cron.d	2008-06-11 07:32:31 UTC (rev 2012)
@@ -1 +1 @@
-0 0 * * *	root	find /var/www/emboss/output -mindepth 1 -maxdepth 1 -atime 1 -exec rm -rf {} \;
+0 0 * * *	root	find /var/www/emboss-explorer/output -mindepth 1 -maxdepth 1 -atime 1 -exec rm -rf {} \;

Modified: trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.install
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.install	2008-06-11 07:31:13 UTC (rev 2011)
+++ trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.install	2008-06-11 07:32:31 UTC (rev 2012)
@@ -6,4 +6,4 @@
 ../../html/style/*			var/www/emboss-explorer/style/
 ../../cgi/emboss			usr/lib/cgi-bin/
 ../../bin/*					usr/bin/
-../../emboss-explorer.conf	etc/
+../emboss-explorer.conf		etc/

Modified: trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.postinst
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.postinst	2008-06-11 07:31:13 UTC (rev 2011)
+++ trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.postinst	2008-06-11 07:32:31 UTC (rev 2012)
@@ -17,7 +17,7 @@
 
 case "$1" in
     configure)
-    	chown -R www-data /var/www/emboss
+    	chown -R www-data /var/www/emboss-explorer
     ;;
 
     abort-upgrade|abort-remove|abort-deconfigure)

Modified: trunk/packages/emboss-explorer/trunk/debian/patches/00list
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/patches/00list	2008-06-11 07:31:13 UTC (rev 2011)
+++ trunk/packages/emboss-explorer/trunk/debian/patches/00list	2008-06-11 07:32:31 UTC (rev 2012)
@@ -1,4 +1,3 @@
 01-fix_examples.dpatch
 02-fix_Conf.pm.dpatch
-03-add_conffile.dpatch
 04-fix_install.dpatch

Deleted: trunk/packages/emboss-explorer/trunk/debian/patches/03-add_conffile.dpatch
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/patches/03-add_conffile.dpatch	2008-06-11 07:31:13 UTC (rev 2011)
+++ trunk/packages/emboss-explorer/trunk/debian/patches/03-add_conffile.dpatch	2008-06-11 07:32:31 UTC (rev 2012)
@@ -1,77 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 04-add_conffile.dpatch by David Paleino <d.paleino at gmail.com>
-##
-## All lines beginning with `## DP:' are a description of the patch.
-## DP: Config file extracted from Conf.pm
-
- at DPATCH@
-diff -urNad emboss-explorer~/emboss-explorer.conf emboss-explorer/emboss-explorer.conf
---- emboss-explorer~/emboss-explorer.conf	1970-01-01 01:00:00.000000000 +0100
-+++ emboss-explorer/emboss-explorer.conf	2007-05-24 11:43:48.000000000 +0200
-@@ -0,0 +1,66 @@
-+# path to the EMBOSS::GUI HTML files
-+our $HTML_PATH = "/var/www/emboss/html";
-+
-+# URL corresponding to $HTML_PATH above
-+our $HTML_URL = "/emboss";
-+
-+# URL specifying the style sheet to use
-+our $STYLE_URL = "$HTML_URL/style/emboss.css";
-+
-+# URL prefix to place before image links
-+our $IMAGE_URL = "$HTML_URL/images";
-+
-+# URL prefix to place before manual links (only used in static pages)
-+our $MANUAL_URL = "$HTML_URL/manual";
-+
-+# path to the EMBOSS::GUI temporary output directory
-+our $OUTPUT_PATH = "$HTML_PATH/output";
-+
-+# URL corresponding to $OUTPUT_PATH above
-+our $OUTPUT_URL = "$HTML_URL/output";
-+
-+# prefix under which EMBOSS was installed
-+our $EMBOSS_PREFIX = "/usr/local";
-+
-+# path to EMBOSS binaries
-+our $EMBOSS_BIN = "$EMBOSS_PREFIX/bin";
-+
-+# path to EMBOSS installation
-+our $EMBOSS_HOME = "$EMBOSS_PREFIX/share/EMBOSS";
-+
-+# path to EMBOSS ACD files
-+our $EMBOSS_ACDROOT = "$EMBOSS_HOME/acd";
-+
-+# path to EMBOSS data
-+our $EMBOSS_DATA = "$EMBOSS_HOME/data";
-+
-+# path to EMBOSS application manuals
-+our $EMBOSS_MANUAL = "$EMBOSS_HOME/doc/html";
-+
-+# list of groups and applications to exclude from the main menu
-+our @EXCLUDED = (
-+	"ACD",
-+	"acdc",
-+	"acdpretty",
-+	"acdtable",
-+	"acdtrace",
-+	"acdvalid",
-+	"UTILS DATABASE CREATION",
-+	"aaindexextract",
-+	"cutgextract",
-+	"printsextract",
-+	"prosextract",
-+	"rebaseextract",
-+	"tfextract",
-+	"UTILS DATABASE INDEXING",
-+	"dbiblast",
-+	"dbifasta",
-+	"dbiflat",
-+	"dbigcg",
-+);
-+
-+# number of seconds to delay between placeholder page refreshes
-+our $REFRESH_DELAY = 1;
-+
-+# whether or not to display using frames
-+our $FRAMES = 1;

Modified: trunk/packages/emboss-explorer/trunk/debian/patches/04-fix_install.dpatch
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/patches/04-fix_install.dpatch	2008-06-11 07:31:13 UTC (rev 2011)
+++ trunk/packages/emboss-explorer/trunk/debian/patches/04-fix_install.dpatch	2008-06-11 07:32:31 UTC (rev 2012)
@@ -6,10 +6,9 @@
 ## DP: hack.
 
 @DPATCH@
-diff -urNad emboss-explorer~/install emboss-explorer/install
---- emboss-explorer~/install	2007-05-25 09:27:10.000000000 +0200
-+++ emboss-explorer/install	2007-05-25 10:10:53.000000000 +0200
-@@ -1,68 +1,25 @@
+--- ./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
  
@@ -20,7 +19,8 @@
 -EOF
 -	exit 1
 -}
--
++HTML_PATH=/var/www/emboss-explorer
+ 
 -prompt() {
 -	echo -e "$1\n\t(default is $2)"
 -	read INPUT
@@ -40,16 +40,11 @@
 -
 -# TODO something fancy to guess the web root?
 -prompt "Where should the EMBOSS Explorer HTML files be installed?" /var/www/html/emboss HTML_PATH
-+EMBOSS_PREFIX=/usr
-+HTML_PATH=/var/www/emboss-explorer
- OUTPUT_PATH=$HTML_PATH/output
+-OUTPUT_PATH=$HTML_PATH/output
 -
 -prompt "What is the URL prefix corresponding to the HTML directory above?" /emboss HTML_URL
-+HTML_URL=/emboss
- OUTPUT_URL=$HTML_URL/output
-+IMAGE_URL=/images/emboss-explorer
-+MANUAL_URL=/doc/emboss-explorer/html
- 
+-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 ]
@@ -64,17 +59,14 @@
 -
 -# munge EMBOSS::GUI::Conf according to the information above...
 -CONF_MODULE=`perl -MEMBOSS::GUI::Conf -e 'print $INC{"EMBOSS/GUI/Conf.pm"}'`
-+CONF_MODULE=$BUILD_DIR/etc/emboss-explorer.conf
- 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='$EMBOSS_PREFIX'; s/(?<=EMBOSS_PREFIX = \")[^\"]*/\$EMBOSS_PREFIX/;
-+	\$IMAGE_URL='$IMAGE_URL'; s/(?<=IMAGE_URL = \")[^\"]*/\$IMAGE_URL/;
-+	\$MANUAL_URL='$MANUAL_URL'; s/(?<=MANUAL_URL = \")[^\"]*/\$MANUAL_URL/;
- " $CONF_MODULE
- 
+-perl -pi -e "
+-	\$HTML_PATH = '$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...
@@ -87,7 +79,7 @@
  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 +28,7 @@
+@@ -71,58 +11,7 @@
      <title>EMBOSS Explorer</title>
    </head>
    <frameset cols=\"170, *\">

Modified: trunk/packages/emboss-explorer/trunk/debian/rules
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/rules	2008-06-11 07:31:13 UTC (rev 2011)
+++ trunk/packages/emboss-explorer/trunk/debian/rules	2008-06-11 07:32:31 UTC (rev 2012)
@@ -4,16 +4,10 @@
 # Uncomment this to turn on verbose mode.
 #export DH_VERBOSE=1
 
-patch: patch-stamp
-patch-stamp:
-	dpatch apply-all
-	touch $@
+include /usr/share/dpatch/dpatch.make
 
-unpatch:
-	dpatch deapply-all
-	rm -rf debian/patched patch-stamp
-
-build: patch
+configure: configure-stamp
+configure-stamp:
 	# the VENDORARCHEXP and INSTALLVENDORARCH
 	# variables are set to avoid the creation
 	# of /usr/lib/perl5
@@ -21,36 +15,34 @@
 		INSTALLDIRS=vendor \
 		VENDORARCHEXP=/usr/share/perl5 \
 		INSTALLVENDORARCH=/usr/share/perl5
+	touch configure-stamp
+
+build: patch configure build-stamp
+build-stamp:
 	$(MAKE)
 	xsltproc -''-nonet /usr/share/sgml/docbook/stylesheet/xsl/nwalsh/manpages/docbook.xsl debian/acdcheck.xml
 	xsltproc -''-nonet /usr/share/sgml/docbook/stylesheet/xsl/nwalsh/manpages/docbook.xsl debian/mkstatic.xml
+	touch build-stamp
 
-clean: unpatch distclean
-distclean:
+clean: unpatch configure
 	dh_testdir
 	dh_testroot
+	$(MAKE) clean
+	dh_clean Makefile.old acdcheck.1 mkstatic.1 build-stamp configure-stamp
 
-	-$(MAKE) clean
-	
-	dh_clean Makefile.old acdcheck.1 mkstatic.1
-
 install: build
 	dh_testdir
 	dh_testroot
 	dh_clean -k -i
 	dh_installdirs -i -A
-
 	$(MAKE) install PREFIX=$(CURDIR)/debian/tmp/usr
-	
-	dh_install --sourcedir=debian/tmp
-	
 	./install
 	
 binary-arch:
 binary-indep: build install
 	dh_testdir
 	dh_testroot
-#	dh_install --sourcedir=debian/tmp
+	dh_install --sourcedir=debian/tmp
 	dh_installchangelogs 
 	dh_installexamples
 	dh_installcron


