[Pkg-emboss-commits] r42 - in emboss-explorer/trunk/debian: . patches

hanska-guest at alioth.debian.org hanska-guest at alioth.debian.org
Sun May 20 13:47:48 UTC 2007 

Author: hanska-guest
Date: 2007-05-20 13:47:48 +0000 (Sun, 20 May 2007)
New Revision: 42

Added:
   emboss-explorer/trunk/debian/emboss-explorer.examples
   emboss-explorer/trunk/debian/patches/
   emboss-explorer/trunk/debian/patches/00list
   emboss-explorer/trunk/debian/patches/01-fix_install.dpatch
   emboss-explorer/trunk/debian/patches/02-fix_examples.dpatch
Removed:
   emboss-explorer/trunk/debian/install-script
Modified:
   emboss-explorer/trunk/debian/control
   emboss-explorer/trunk/debian/copyright
   emboss-explorer/trunk/debian/rules
Log:
Added some patching, examples, EMBOSS:ACD manpage moved to
libemboss-acd-perl, some fixing in debian/rules, ...


Modified: emboss-explorer/trunk/debian/control
===================================================================
--- emboss-explorer/trunk/debian/control	2007-05-18 12:53:42 UTC (rev 41)
+++ emboss-explorer/trunk/debian/control	2007-05-20 13:47:48 UTC (rev 42)
@@ -11,7 +11,7 @@
 
 Package: emboss-explorer
 Architecture: all
-Depends: ${misc:Depends}, ${perl:Depends}, libparse-recdescent-perl, libmailtools-perl, emboss
+Depends: ${misc:Depends}, ${perl:Depends}, libparse-recdescent-perl, libmailtools-perl, emboss, libemboss-acd-perl, emboss-data
 Recommends: emboss-doc
 Description: web-based GUI to EMBOSS
  EMBOSS explorer is a web-based graphical user interface

Modified: emboss-explorer/trunk/debian/copyright
===================================================================
--- emboss-explorer/trunk/debian/copyright	2007-05-18 12:53:42 UTC (rev 41)
+++ emboss-explorer/trunk/debian/copyright	2007-05-20 13:47:48 UTC (rev 42)
@@ -9,7 +9,7 @@
 
 Copyright: 
 
-    (C) 2004 Luke McCarthy
+    (C) 2004-2006 Luke McCarthy
 
 License:
 

Added: emboss-explorer/trunk/debian/emboss-explorer.examples
===================================================================
--- emboss-explorer/trunk/debian/emboss-explorer.examples	                        (rev 0)
+++ emboss-explorer/trunk/debian/emboss-explorer.examples	2007-05-20 13:47:48 UTC (rev 42)
@@ -0,0 +1 @@
+t/ACD.t

Deleted: emboss-explorer/trunk/debian/install-script
===================================================================
--- emboss-explorer/trunk/debian/install-script	2007-05-18 12:53:42 UTC (rev 41)
+++ emboss-explorer/trunk/debian/install-script	2007-05-20 13:47:48 UTC (rev 42)
@@ -1,47 +0,0 @@
-#!/bin/sh
-BUILD_DIR=./debian/emboss-explorer
-
-EMBOSS_PREFIX=/usr
-HTML_PATH=/var/www/emboss
-OUTPUT_PATH=$HTML_PATH/output
-HTML_URL=/emboss
-OUTPUT_URL=$HTML_URL/output
-CGI_PATH=/usr/lib/cgi-bin/emboss
-IMAGE_URL=/images/emboss-explorer
-MANUAL_URL=/doc/emboss-explorer/html
-
-if [ -d $CGI_PATH ]
-then
-	CGI_DIR=$CGI_PATH
-	CGI_PATH=$CGI_DIR/emboss
-else
-	CGI_DIR=${CGI_PATH%/*}
-fi
-
-CGI_URL=/cgi-bin/emboss
-
-# 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/usr/share/perl5/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='$EMBOSS_PREFIX'; s/(?<=EMBOSS_PREFIX = \")[^\"]*/\$EMBOSS_PREFIX/;
-	\$IMAGE_URL='$IMAGE_URL'; s/(?<=IMAGE_URL = \")[^\"]*/\$IMAGE_URL/;
-	\$MANUAL_URL='$MANUAL_URL'; s/(?<=MANUAL_URL = \")[^\"]*/\$MANUAL_URL/;
-" $CONF_MODULE
-
-echo creating HTML index file at $HTML_PATH/index.html...
-echo "<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Frameset//EN\"
- \"http://www.w3.org/TR/xhtml1/DTD/xhtml1-frameset.dtd\">
-<html xmlns='http://www.w3.org/1999/xhtml' xml:lang='en' lang='en'>
-  <head>
-    <title>EMBOSS Explorer</title>
-  </head>
-  <frameset cols=\"170, *\">
-    <frame src=\"$CGI_URL/menu\" name=\"menu\" />
-    <frame src=\"$CGI_URL/intro\" name=\"main\" />
-  </frameset>
-</html>" >$BUILD_DIR$HTML_PATH/index.html

Added: emboss-explorer/trunk/debian/patches/00list
===================================================================
--- emboss-explorer/trunk/debian/patches/00list	                        (rev 0)
+++ emboss-explorer/trunk/debian/patches/00list	2007-05-20 13:47:48 UTC (rev 42)
@@ -0,0 +1,2 @@
+01-fix_install.dpatch
+02-fix_examples.dpatch

Added: emboss-explorer/trunk/debian/patches/01-fix_install.dpatch
===================================================================
--- emboss-explorer/trunk/debian/patches/01-fix_install.dpatch	                        (rev 0)
+++ emboss-explorer/trunk/debian/patches/01-fix_install.dpatch	2007-05-20 13:47:48 UTC (rev 42)
@@ -0,0 +1,149 @@
+#! /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.
+
+ at DPATCH@
+diff -urNad emboss-explorer~/install emboss-explorer/install
+--- emboss-explorer~/install	2006-11-13 01:55:53.000000000 +0100
++++ emboss-explorer/install	2007-05-20 15:21:16.000000000 +0200
+@@ -1,38 +1,15 @@
+ #!/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
+-}
+-
+-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?" ${EMBOSS_PREFIX:-/usr/local} EMBOSS_PREFIX
+-
+-# TODO something fancy to guess the web root?
+-prompt "Where should the EMBOSS Explorer HTML files be installed?" /var/www/html/emboss HTML_PATH
++EMBOSS_PREFIX=/usr
++HTML_PATH=/var/www/emboss
+ OUTPUT_PATH=$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
+-
+-prompt "Where should the EMBOSS Explorer CGI script be installed?" /var/www/cgi-bin/emboss CGI_PATH
++CGI_PATH=/usr/lib/cgi-bin/emboss
++IMAGE_URL=/images/emboss-explorer
++MANUAL_URL=/doc/emboss-explorer/html
++CGI_URL=/cgi-bin/emboss
+ 
+ if [ -d $CGI_PATH ]
+ then
+@@ -42,27 +19,23 @@
+ 	CGI_DIR=${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"}'`
++#
++# we haven't installed emboss-explorer yet, so the following perl
++# line won't work (thus setting CONF_MODULE in a static-way):
++#
++# CONF_MODULE=`perl -MEMBOSS::GUI::Conf -e 'print $INC{"EMBOSS/GUI/Conf.pm"}'`
++CONF_MODULE=$BUILD_DIR/usr/share/perl5/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='$EMBOSS_PREFIX'; s/(?<=EMBOSS_PREFIX = \")[^\"]*/\$EMBOSS_PREFIX/;
++	\$IMAGE_URL='$IMAGE_URL'; s/(?<=IMAGE_URL = \")[^\"]*/\$IMAGE_URL/;
++	\$MANUAL_URL='$MANUAL_URL'; s/(?<=MANUAL_URL = \")[^\"]*/\$MANUAL_URL/;
+ " $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 $HTML_PATH/index.html...
+ echo "<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Frameset//EN\"
+  \"http://www.w3.org/TR/xhtml1/DTD/xhtml1-frameset.dtd\">
+@@ -75,54 +48,3 @@
+     <frame src=\"$CGI_URL/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


Property changes on: emboss-explorer/trunk/debian/patches/01-fix_install.dpatch
___________________________________________________________________
Name: svn:executable
   + *

Added: emboss-explorer/trunk/debian/patches/02-fix_examples.dpatch
===================================================================
--- emboss-explorer/trunk/debian/patches/02-fix_examples.dpatch	                        (rev 0)
+++ emboss-explorer/trunk/debian/patches/02-fix_examples.dpatch	2007-05-20 13:47:48 UTC (rev 42)
@@ -0,0 +1,19 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 02-fix_examples.dpatch by David Paleino <d.paleino at gmail.com>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: No description.
+
+ at DPATCH@
+diff -urNad emboss-explorer~/t/ACD.t emboss-explorer/t/ACD.t
+--- emboss-explorer~/t/ACD.t	2006-11-13 00:38:39.000000000 +0100
++++ emboss-explorer/t/ACD.t	2007-05-20 15:33:09.000000000 +0200
+@@ -15,7 +15,7 @@
+ BEGIN {
+ 	# locate the EMBOSS ACD files in order to validate against them...
+ 	#
+-	@ACDFILES = glob "/usr/local/share/EMBOSS/acd/*.acd";
++	@ACDFILES = glob "/usr/share/EMBOSS/acd/*.acd";
+ 
+ 	$XHTML = EMBOSS::GUI::XHTML->new(
+ 		script_url => 'dummy'


Property changes on: emboss-explorer/trunk/debian/patches/02-fix_examples.dpatch
___________________________________________________________________
Name: svn:executable
   + *

Modified: emboss-explorer/trunk/debian/rules
===================================================================
--- emboss-explorer/trunk/debian/rules	2007-05-18 12:53:42 UTC (rev 41)
+++ emboss-explorer/trunk/debian/rules	2007-05-20 13:47:48 UTC (rev 42)
@@ -4,7 +4,16 @@
 # Uncomment this to turn on verbose mode.
 #export DH_VERBOSE=1
 
-build:
+patch: patch-stamp
+patch-stamp:
+	dpatch apply-all
+	touch $@
+
+unpatch:
+	dpatch deapply-all
+	rm -rf debian/patched patch-stamp
+
+build: patch
 	# the VENDORARCHEXP and INSTALLVENDORARCH
 	# variables are set to avoid the creation
 	# of /usr/lib/perl5
@@ -16,7 +25,8 @@
 	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
 
-clean:
+clean: unpatch distclean
+distclean:
 	dh_testdir
 	dh_testroot
 
@@ -30,29 +40,33 @@
 	dh_clean -k -i
 	dh_installdirs -i -A
 
-	$(MAKE) install PREFIX=$(CURDIR)/debian/emboss-explorer/usr
+	$(MAKE) install PREFIX=$(CURDIR)/debian/tmp/usr
 	
-	-install -m 644 html/* $(CURDIR)/debian/emboss-explorer/var/www/emboss/
-	install -m 644 html/images/* $(CURDIR)/debian/emboss-explorer/usr/share/images/emboss-explorer/
-	install -m 644 html/style/* $(CURDIR)/debian/emboss-explorer/var/www/emboss/style/
-	install -m 755 cgi/emboss $(CURDIR)/debian/emboss-explorer/usr/lib/cgi-bin/emboss
-	install -m 755 bin/* $(CURDIR)/debian/emboss-explorer/usr/bin
-	mv $(CURDIR)/debian/emboss-explorer/usr/share/perl5/EMBOSS/ACD.pm $(CURDIR)/debian/libemboss-acd-perl/usr/share/perl5/EMBOSS/ACD.pm
+	# let's create the same dirs into debian/tmp/
+	mkdir -p $(CURDIR)/debian/tmp/usr/bin \
+			$(CURDIR)/debian/tmp/usr/lib/cgi-bin \
+			$(CURDIR)/debian/tmp/usr/share/images/emboss-explorer \
+			$(CURDIR)/debian/tmp/var/www/emboss/output \
+			$(CURDIR)/debian/tmp/var/www/emboss/style \
+			$(CURDIR)/debian/tmp/usr/share/perl5/EMBOSS/
 
+	-install -m 644 html/* $(CURDIR)/debian/tmp/var/www/emboss/
+	install -m 644 html/images/* $(CURDIR)/debian/tmp/usr/share/images/emboss-explorer/
+	install -m 644 html/style/* $(CURDIR)/debian/tmp/var/www/emboss/style/
+	install -m 755 cgi/emboss $(CURDIR)/debian/tmp/usr/lib/cgi-bin/emboss
+	install -m 755 bin/* $(CURDIR)/debian/tmp/usr/bin
+
 	# fixing permissions
-	chmod a+rwx $(CURDIR)/debian/emboss-explorer/var/www/emboss/output/
+	chmod a+rwx $(CURDIR)/debian/tmp/var/www/emboss/output/
 
-	# some additional fixing is done in debian/install-script
-	chmod a+x debian/install-script
-	debian/install-script	
-
 binary-arch:
-
 binary-indep: build install
 	dh_testdir
 	dh_testroot
+	dh_install --sourcedir=debian/tmp
 	dh_installchangelogs 
-	dh_installdocs README
+	dh_installexamples
+	dh_installdocs
 	dh_installman
 	dh_link
 	dh_strip

More information about the Pkg-emboss-commits mailing list