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
$perl,@inc,$metadb_script,"--dsn=DBI:SQLite:debian/gbrowse/usr/share/gbrowse2/databases/users.sqlite";
++ system
$perl,@inc,$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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