[med-svn] r6420 - in trunk/packages/gbrowse/trunk/debian: . patches

olivier sallou osallou-guest at alioth.debian.org
Fri Apr 1 09:52:23 UTC 2011 

Author: osallou-guest
Date: 2011-04-01 09:52:22 +0000 (Fri, 01 Apr 2011)
New Revision: 6420

Added:
   trunk/packages/gbrowse/trunk/debian/get-orig-source
Modified:
   trunk/packages/gbrowse/trunk/debian/README.Debian
   trunk/packages/gbrowse/trunk/debian/copyright
   trunk/packages/gbrowse/trunk/debian/gbrowse-data.postinst
   trunk/packages/gbrowse/trunk/debian/links
   trunk/packages/gbrowse/trunk/debian/patches/debian-packaging-patch
   trunk/packages/gbrowse/trunk/debian/postinst
   trunk/packages/gbrowse/trunk/debian/postrm
   trunk/packages/gbrowse/trunk/debian/rules
   trunk/packages/gbrowse/trunk/debian/watch
Log:
remove contribs for licensing issues, update scripts to support arguments, update path to gbrowse instead of gbrowse2

Modified: trunk/packages/gbrowse/trunk/debian/README.Debian
===================================================================
--- trunk/packages/gbrowse/trunk/debian/README.Debian	2011-04-01 08:09:51 UTC (rev 6419)
+++ trunk/packages/gbrowse/trunk/debian/README.Debian	2011-04-01 09:52:22 UTC (rev 6420)
@@ -5,4 +5,4 @@
  has been installed in /etc/apache2/conf.d to map URLs to GBrowse directories.
  In other cases (other web server, apache not installed...), one should configure the web
  server to trigger gbrowse. An apache2 template is available in configration directory
- (/etc/gbrowse2/apache2.conf).
+ (/etc/gbrowse/apache2.conf).

Modified: trunk/packages/gbrowse/trunk/debian/copyright
===================================================================
--- trunk/packages/gbrowse/trunk/debian/copyright	2011-04-01 08:09:51 UTC (rev 6419)
+++ trunk/packages/gbrowse/trunk/debian/copyright	2011-04-01 09:52:22 UTC (rev 6420)
@@ -95,7 +95,7 @@
 
 Files: htdocs/css/dropdown/default_theme.css htdocs/css/dropdown/dropdown.css
 Copyright: © 2008 Live Web Institute. All Rights Reserved.
-License: unknown
+License: GPL-3
 
 Files: docs/pod/INSTALL.MacOSX.pod
 Copyright @ 2003 Cold Spring Harbor Laboratory

Modified: trunk/packages/gbrowse/trunk/debian/gbrowse-data.postinst
===================================================================
--- trunk/packages/gbrowse/trunk/debian/gbrowse-data.postinst	2011-04-01 08:09:51 UTC (rev 6419)
+++ trunk/packages/gbrowse/trunk/debian/gbrowse-data.postinst	2011-04-01 09:52:22 UTC (rev 6420)
@@ -5,9 +5,21 @@
 # Source debconf library.
 . /usr/share/debconf/confmodule
 
-#DEBHELPER#
+case "$1" in
+    configure)
+      chown -R root:www-data /usr/share/gbrowse/databases
+      chmod -R 770 /usr/share/gbrowse/databases
+   ;;
 
+    abort-upgrade|abort-remove|abort-deconfigure)
+    ;;
 
-chown -R root:www-data /usr/share/gbrowse2/databases
-chmod -R 770 /usr/share/gbrowse2/databases
+    *)
+        echo "postinst called with unknown argument \`$1'" >&2
+        exit 1
+    ;;
+esac
 
+
+#DEBHELPER#
+

Added: trunk/packages/gbrowse/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/gbrowse/trunk/debian/get-orig-source	                        (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/get-orig-source	2011-04-01 09:52:22 UTC (rev 6420)
@@ -0,0 +1,27 @@
+#!/bin/bash
+
+set -e
+
+PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+VERSION=`uscan --rename --verbose --force-download | 
+    grep "Newest version on remote site is .* local version is .*" | 
+    head -n 1 | 
+    sed "s/Newest version on remote site is \([a-z0-9.]\+\),.*/\1/"`
+
+mkdir -p ../tarballs
+cd ../tarballs
+
+UTAR="${PKG}_${VERSION}.orig.tar.gz"
+mv ../${UTAR} .
+tar -xzf ${UTAR}
+
+mv GBrowse-${VERSION} $PKG-${VERSION}.orig # Requested by Developers Reference 3.4.4 §6.7.8.2
+
+cd $PKG-${VERSION}.orig
+rm -rf contrib
+cd ..
+
+rm $UTAR
+
+GZIP="--best --no-name" tar -czf "$PKG"_"$VERSION".orig.tar.gz "${PKG}-${VERSION}.orig"
+rm -rf "${PKG}-${VERSION}.orig"


Property changes on: trunk/packages/gbrowse/trunk/debian/get-orig-source
___________________________________________________________________
Added: svn:executable
   + *

Modified: trunk/packages/gbrowse/trunk/debian/links
===================================================================
--- trunk/packages/gbrowse/trunk/debian/links	2011-04-01 08:09:51 UTC (rev 6419)
+++ trunk/packages/gbrowse/trunk/debian/links	2011-04-01 09:52:22 UTC (rev 6420)
@@ -1,2 +1,2 @@
-/usr/share/javascript/prototype/prototype.js usr/share/gbrowse2/htdocs/js/prototype.js
-/usr/share/javascript/scriptaculous/scriptaculous.js usr/share/gbrowse2/htdocs/js/scriptaculous.js
+/usr/share/javascript/prototype/prototype.js usr/share/gbrowse/htdocs/js/prototype.js
+/usr/share/javascript/scriptaculous/scriptaculous.js usr/share/gbrowse/htdocs/js/scriptaculous.js

Modified: trunk/packages/gbrowse/trunk/debian/patches/debian-packaging-patch
===================================================================
--- trunk/packages/gbrowse/trunk/debian/patches/debian-packaging-patch	2011-04-01 08:09:51 UTC (rev 6419)
+++ trunk/packages/gbrowse/trunk/debian/patches/debian-packaging-patch	2011-04-01 09:52:22 UTC (rev 6420)
@@ -17,7 +17,7 @@
 +.PP
 +.SH CONFIGURATION
 +.B gbrowse2
-+Configuration files are located in /etc/gbrowse2. Main configuration file is GBrowse.conf. It contains the global configuration elements. Specific configuration files are located in the same directory per data bank. For more details, one should refer to the GBrowse documentation.
++Configuration files are located in /etc/gbrowse. Main configuration file is GBrowse.conf. It contains the global configuration elements. Specific configuration files are located in the same directory per data bank. For more details, one should refer to the GBrowse documentation.
 + Installation is provided with a Yeast genome sample.
 +.PP
 +.SH DESCRIPTION
@@ -118,7 +118,7 @@
 +    my $metadb_script = File::Spec->catfile("bin", "gbrowse_metadb_config.pl");
 +    my $perl          = $self->perl;
 +    my @inc           = map{"-I$_"} split ':',$self->added_to_INC;
-+    system $perl, at inc,$metadb_script,"--dsn=DBI:SQLite:debian/gbrowse/usr/share/gbrowse2/databases/users.sqlite";
++    system $perl, at inc,$metadb_script,"--dsn=DBI:SQLite:debian/gbrowse/usr/share/gbrowse/databases/users.sqlite";
 +
 +}
 +

Modified: trunk/packages/gbrowse/trunk/debian/postinst
===================================================================
--- trunk/packages/gbrowse/trunk/debian/postinst	2011-04-01 08:09:51 UTC (rev 6419)
+++ trunk/packages/gbrowse/trunk/debian/postinst	2011-04-01 09:52:22 UTC (rev 6420)
@@ -7,30 +7,30 @@
 
 case "$1" in
     configure)
-if [ -e /var/cache/gbrowse2 ]
+if [ -e /var/cache/gbrowse ]
 then
  echo "Dir already present, skip it"
 else
-mkdir -p /var/cache/gbrowse2
+mkdir -p /var/cache/gbrowse
 fi
 
-chown -R root:www-data /usr/share/gbrowse2/databases
-chmod -R 770 /usr/share/gbrowse2/databases
-chown -R root:www-data /var/cache/gbrowse2
-chmod -R 770 /var/cache/gbrowse2
+chown -R root:www-data /usr/share/gbrowse/databases
+chmod -R 770 /usr/share/gbrowse/databases
+chown -R root:www-data /var/cache/gbrowse
+chmod -R 770 /var/cache/gbrowse
 # Initialize account database
 perl /usr/bin/gbrowse_metadb_config
-chown -R www-data:www-data /var/cache/gbrowse2/sessions
-chown www-data:www-data /usr/share/gbrowse2/databases/users.sqlite
+chown -R www-data:www-data /var/cache/gbrowse/sessions
+chown www-data:www-data /usr/share/gbrowse/databases/users.sqlite
 
 
 if [ -e /etc/apache2/conf.d ]
 then
- if [ -e /etc/apache2/conf.d/gbrowse2 ]
+ if [ -e /etc/apache2/conf.d/gbrowse ]
  then
    echo "Apache config already set, keeping original"
  else
-   ln -s /etc/gbrowse2/apache2.conf /etc/apache2/conf.d/gbrowse2
+   ln -s /etc/gbrowse/apache2.conf /etc/apache2/conf.d/gbrowse
    echo "Warning, apache2 must be restarted to take into account the configuration"
  fi
 fi

Modified: trunk/packages/gbrowse/trunk/debian/postrm
===================================================================
--- trunk/packages/gbrowse/trunk/debian/postrm	2011-04-01 08:09:51 UTC (rev 6419)
+++ trunk/packages/gbrowse/trunk/debian/postrm	2011-04-01 09:52:22 UTC (rev 6420)
@@ -7,16 +7,16 @@
 
 case "$1" in
     purge|remove|upgrade|failed-upgrade|abort-install|abort-upgrade|disappear)
-rm -rf /var/cache/gbrowse2
+rm -rf /var/cache/gbrowse
 
-if [ -e /etc/apache2/conf.d/gbrowse2 ]
+if [ -e /etc/apache2/conf.d/gbrowse ]
 then
- rm /etc/apache2/conf.d/gbrowse2
+ rm /etc/apache2/conf.d/gbrowse
 fi
 
-if [ -e /usr/share/gbrowse2 ]
+if [ -e /usr/share/gbrowse ]
 then
-rm -rf /usr/share/gbrowse2
+rm -rf /usr/share/gbrowse
 fi
 
 if [ "$1" = "purge" ]; then

Modified: trunk/packages/gbrowse/trunk/debian/rules
===================================================================
--- trunk/packages/gbrowse/trunk/debian/rules	2011-04-01 08:09:51 UTC (rev 6419)
+++ trunk/packages/gbrowse/trunk/debian/rules	2011-04-01 09:52:22 UTC (rev 6420)
@@ -6,7 +6,7 @@
 
 override_dh_auto_build:
 	echo "Skipping this step"
-	#perl Build.PL --install_path lib=/usr/lib/perl5  --conf=/etc/gbrowse2 --htdocs=/usr/share/gbrowse2/htdocs --tmp=/var/cache/gbrowse2 --databases=/usr/share/gbrowse2/databases --cgibin=/usr/lib/cgi-bin/gbrowse2 --www-user=www-data  --installetc=y
+	#perl Build.PL --install_path lib=/usr/lib/perl5  --conf=/etc/gbrowse --htdocs=/usr/share/gbrowse/htdocs --tmp=/var/cache/gbrowse --databases=/usr/share/gbrowse/databases --cgibin=/usr/lib/cgi-bin/gbrowse --www-user=www-data  --installetc=y
 	#dh_auto_build
 
 override_dh_auto_test:
@@ -14,28 +14,30 @@
 
 override_dh_auto_install:
 	echo "Using specific install"
-	perl Build.PL --conf=/etc/gbrowse2 --htdocs=/usr/share/gbrowse2/htdocs --tmp=/var/cache/gbrowse2 --databases=/usr/share/gbrowse2/databases --cgibin=/usr/lib/cgi-bin/gbrowse2 --www-user=www-data  
+	perl Build.PL --conf=/etc/gbrowse --htdocs=/usr/share/gbrowse/htdocs --tmp=/var/cache/gbrowse --databases=/usr/share/gbrowse/databases --cgibin=/usr/lib/cgi-bin/gbrowse --www-user=www-data  
 	./Build  --install_base=debian/gbrowse debianinstall
-	./Build   apache_conf > debian/gbrowse/etc/gbrowse2/apache2.conf
-	perl Build.PL --conf=/etc/gbrowse2 --htdocs=/usr/share/gbrowse2/htdocs --tmp=/var/cache/gbrowse2 --databases=/usr/share/gbrowse2/databases --cgibin=/usr/lib/cgi-bin/gbrowse2 --www-user=www-data  --installetc=y
+	./Build   apache_conf > debian/gbrowse/etc/gbrowse/apache2.conf
+	perl Build.PL --conf=/etc/gbrowse --htdocs=/usr/share/gbrowse/htdocs --tmp=/var/cache/gbrowse --databases=/usr/share/gbrowse/databases --cgibin=/usr/lib/cgi-bin/gbrowse --www-user=www-data  --installetc=y
 	./Build  --install_base=debian/gbrowse install_slave
 	mkdir -p debian/gbrowse/usr/lib/perl5
 	mv debian/gbrowse/lib/perl5/*/* debian/gbrowse/usr/lib/perl5/
 	rm -rf debian/gbrowse/lib
 	rm -f debian/gbrowse/usr/share/doc/gbrowse/INSTALL
 	rm -f debian/gbrowse/usr/lib/perl5/auto/GBrowse/.packlist
-	rm -f debian/gbrowse/usr/share/gbrowse2/htdocs/js/prototype.js
-	rm -f debian/gbrowse/usr/share/gbrowse2/htdocs/js/scriptaculous.js
-	chmod 644 debian/gbrowse/etc/gbrowse2/MobyServices/text_xml_renderer.pm
-	chmod 644 debian/gbrowse/etc/gbrowse2/synteny/oryza.synconf.disabled
+	rm -f debian/gbrowse/usr/share/gbrowse/htdocs/js/prototype.js
+	rm -f debian/gbrowse/usr/share/gbrowse/htdocs/js/scriptaculous.js
+	chmod 644 debian/gbrowse/etc/gbrowse/MobyServices/text_xml_renderer.pm
+	chmod 644 debian/gbrowse/etc/gbrowse/synteny/oryza.synconf.disabled
 	chmod 755 debian/gbrowse/etc/default/gbrowse-slave
 	#Rename pl scripts in bin
 	rename 's/\.pl//' debian/gbrowse/bin/*.pl
 	mv debian/gbrowse/bin debian/gbrowse/usr/bin
 	# Remove databases, keep it as additional package
-	cp debian/gbrowse/usr/share/gbrowse2/databases/users.sqlite debian/gbrowse/usr/share/gbrowse2/
-	rm -rf debian/gbrowse/usr/share/gbrowse2/databases/*
-	mv debian/gbrowse/usr/share/gbrowse2/users.sqlite debian/gbrowse/usr/share/gbrowse2/databases/
+	touch debian/gbrowse/usr/share/gbrowse/databases/users.sqlite
+	cp debian/gbrowse/usr/share/gbrowse/databases/users.sqlite debian/gbrowse/usr/share/gbrowse/
+	rm -rf debian/gbrowse/usr/share/gbrowse/databases/*
+	mv debian/gbrowse/usr/share/gbrowse/users.sqlite debian/gbrowse/usr/share/gbrowse/databases/
+   
 
 
 override_dh_installman:
@@ -51,3 +53,5 @@
 override_dh_auto_build-gbrowse-data:
 	#Skip
 
+get-orig-source:
+	. debian/get-orig-source

Modified: trunk/packages/gbrowse/trunk/debian/watch
===================================================================
--- trunk/packages/gbrowse/trunk/debian/watch	2011-04-01 08:09:51 UTC (rev 6419)
+++ trunk/packages/gbrowse/trunk/debian/watch	2011-04-01 09:52:22 UTC (rev 6420)
@@ -1,2 +1,2 @@
 version=3
-http://search.cpan.org/dist/GBrowse/   .*/GBrowse-v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$
+http://search.cpan.org/dist/GBrowse .*/GBrowse-v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip) debian uupdate

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