[med-svn] r5757 - trunk/packages/ensembl/ensembl/57/debian

Richard Holland holland-guest at alioth.debian.org
Sat Jan 29 18:53:14 UTC 2011 

Author: holland-guest
Date: 2011-01-29 18:53:10 +0000 (Sat, 29 Jan 2011)
New Revision: 5757

Added:
   trunk/packages/ensembl/ensembl/57/debian/ensembl.templates
Modified:
   trunk/packages/ensembl/ensembl/57/debian/control
   trunk/packages/ensembl/ensembl/57/debian/ensembl.dirs
   trunk/packages/ensembl/ensembl/57/debian/ensembl.links
   trunk/packages/ensembl/ensembl/57/debian/ensembl.postinst
   trunk/packages/ensembl/ensembl/57/debian/init.d
   trunk/packages/ensembl/ensembl/57/debian/prepare_ensembl_source_packages.sh
Log:
Made changes to make Ensembl install properly (issues with db_get and missing templates, amongst others.)


Modified: trunk/packages/ensembl/ensembl/57/debian/control
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/control	2011-01-29 18:41:41 UTC (rev 5756)
+++ trunk/packages/ensembl/ensembl/57/debian/control	2011-01-29 18:53:10 UTC (rev 5757)
@@ -5,7 +5,6 @@
 Uploaders: Richard Holland <holland at eaglegenomics.com>, Steffen Moeller <moeller at debian.org>
 DM-Upload-Allowed: yes
 Build-Depends: debhelper (>= 7.0.50~)
-Build-Depends-Indep: mysql-client
 Standards-Version: 3.9.1.0
 Homepage: http://www.ensembl.org
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/ensembl/ensembl/57/?rev=0&sc=0
@@ -14,7 +13,7 @@
 Package: ensembl
 Architecture: all
 Pre-Depends: debconf
-Depends: ${shlibs:Depends}, ${misc:Depends}, apache2-mpm-prefork, csh, expat, perl, libcgi-pm-perl, libcgi-session-perl, libdb-file-lock-perl, libdbd-mysql, perl-modules, ensembl-bin, libensembl-core-perl,libensembl-functgenomics-perl,libensembl-compara-perl,libensembl-external-perl,libensembl-variation-perl, tcsh, liblwp-parallel-perl, mysql-server
+Depends: ${shlibs:Depends}, ${misc:Depends}, apache2-mpm-prefork, csh, expat, perl, libcgi-pm-perl, libcgi-session-perl, libdb-file-lock-perl, libdbd-mysql, perl-modules, ensembl-bin, libensembl-core-perl,libensembl-functgenomics-perl,libensembl-compara-perl,libensembl-external-perl,libensembl-variation-perl, tcsh, liblwp-parallel-perl, mysql-server, mysql-client
 Recommends: ttf-mscorefonts-installer, acedb-other-dotter, libcgi-ajax-perl, libcache-memcached-perl, libclass-dbi-sweet-perl, libclass-std-perl, libclass-std-utils-perl, libcompress-bzip2-perl, libfile-spec-perl, libdata-uuid-libuuid-perl, libgd-text-perl, libhash-merge-perl, libhtml-parser-perl, liblist-moreutils-perl, liblog-log4perl-perl, libmailtools-perl, libwww-curl-perl, libapache2-mod-perl2, libnumber-format-perl, libgd-gd2-noxpm-perl, libpdf-api2-perl, libsys-hostname-long-perl, libtemplate-plugin-number-format-perl, libxml-dom-perl, libxml-rss-perl, libxml-simple-perl, libbsd-resource-perl, libxml-xpath-perl, libxml-atom-perl, libjson-perl, libclass-data-inheritable-perl, libconfig-inifiles-perl, libdevel-stacktrace-perl, libexception-class-perl, libhtml-template-perl, libimage-size-perl, libio-string-perl, libipc-run-perl, libxml-libxml-perl, libole-storage-lite-perl, libparse-recdescent-perl, libspreadsheet-writeexcel-perl, libmime-types-perl, libmath-bezier-perl, librtf-writer-perl, libbio-das-lite-perl, bioperl1.2.3|bioperl
 Suggests: ksh | mksh | pdksh | zsh
 Description: Installs a basic Ensembl 57 genome browser.

Modified: trunk/packages/ensembl/ensembl/57/debian/ensembl.dirs
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/ensembl.dirs	2011-01-29 18:41:41 UTC (rev 5756)
+++ trunk/packages/ensembl/ensembl/57/debian/ensembl.dirs	2011-01-29 18:53:10 UTC (rev 5757)
@@ -7,3 +7,5 @@
 var/cache
 var/cache/ensembl
 var/cache/ensembl/img-cache
+var/tmp/ensembl/img-tmp
+var/tmp/ensembl/tmp

Modified: trunk/packages/ensembl/ensembl/57/debian/ensembl.links
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/ensembl.links	2011-01-29 18:41:41 UTC (rev 5756)
+++ trunk/packages/ensembl/ensembl/57/debian/ensembl.links	2011-01-29 18:53:10 UTC (rev 5757)
@@ -1,5 +1,4 @@
 /usr/share/ensembl/logs /var/log/ensembl
 /usr/share/ensembl/img-cache /var/cache/ensembl/img-cache
-# should be created at start time, not now.
-#/usr/share/ensembl/img-tmp /var/tmp/ensembl/img-tmp
-#/usr/share/ensembl/tmp /var/tmp/ensembl/tmp
+/usr/share/ensembl/img-tmp /var/tmp/ensembl/img-tmp
+/usr/share/ensembl/tmp /var/tmp/ensembl/tmp

Modified: trunk/packages/ensembl/ensembl/57/debian/ensembl.postinst
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/ensembl.postinst	2011-01-29 18:41:41 UTC (rev 5756)
+++ trunk/packages/ensembl/ensembl/57/debian/ensembl.postinst	2011-01-29 18:53:10 UTC (rev 5757)
@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/sh 
 # postinst script for ensembl
 #
 # see: dh_installdeb(1)
@@ -54,7 +54,6 @@
 	echo "Configuring Apache."
 	db_get ensembl/port
 	ensemblPort="$RET"
-	sed -i "s/__USER_ENSEMBL_PORT__/$ensemblPort/g" /usr/share/ensembl/conf/Plugins.pm /usr/share/ensembl/public-plugins/mirror/conf/SiteDefs.pm
 
 	echo "Configuring Ensembl web user database."
 	db_get ensembl/webuserdbhost
@@ -67,12 +66,9 @@
 	webUserDbUser="$RET"
 	db_get ensembl/webuserdbpwd
 	webUserDbPwd="$RET"
-	sed -i "s/__USER_ENS_DB_HOST__/$webUserDbHost/g" /usr/share/ensembl/conf/Plugins.pm /usr/share/ensembl/public-plugins/mirror/conf/SiteDefs.pm
-	sed -i "s/__USER_ENS_DB_PORT__/$webUserDbPort/g" /usr/share/ensembl/conf/Plugins.pm /usr/share/ensembl/public-plugins/mirror/conf/SiteDefs.pm
-	sed -i "s/__USER_ENS_DB_NAME__/$webUserDbName/g" /usr/share/ensembl/conf/Plugins.pm /usr/share/ensembl/public-plugins/mirror/conf/SiteDefs.pm
-	sed -i "s/__USER_ENS_DB_USER__/$webUserDbUser/g" /usr/share/ensembl/conf/Plugins.pm /usr/share/ensembl/public-plugins/mirror/conf/SiteDefs.pm
-	sed -i "s/__USER_ENS_DB_PWD__/$webUserDbPwd/g" /usr/share/ensembl/conf/Plugins.pm /usr/share/ensembl/public-plugins/mirror/conf/SiteDefs.pm
 
+	sed -i "s/__USER_ENSEMBL_PORT__/$ensemblPort/g;s/__USER_ENS_DB_HOST__/$webUserDbHost/g;s/__USER_ENS_DB_PORT__/$webUserDbPort/g;s/__USER_ENS_DB_NAME__/$webUserDbName/g;s/__USER_ENS_DB_USER__/$webUserDbUser/g;s/__USER_ENS_DB_PWD__/$webUserDbPwd/g" /usr/share/ensembl/conf/Plugins.pm /usr/share/ensembl/public-plugins/mirror/conf/SiteDefs.pm
+
 	db_get ensembl/webuserdbexistyn
 	existYn="$RET"
 	if [ "true" = "$existYn" ]
@@ -121,6 +117,16 @@
 # dh_installdeb will replace this with shell code automatically
 # generated by other debhelper scripts.
 
-#DEBHELPER#
+# Automatically added by dh_installinit
+if [ -x "/etc/init.d/ensembl" ]; then
+	update-rc.d ensembl defaults >/dev/null
+	if [ -x "`which invoke-rc.d 2>/dev/null`" ]; then
+		invoke-rc.d ensembl start || exit $?
+	else
+		/etc/init.d/ensembl start || exit $?
+	fi
+fi
+# End automatically added section
 
+
 exit 0

Added: trunk/packages/ensembl/ensembl/57/debian/ensembl.templates
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/ensembl.templates	                        (rev 0)
+++ trunk/packages/ensembl/ensembl/57/debian/ensembl.templates	2011-01-29 18:53:10 UTC (rev 5757)
@@ -0,0 +1,54 @@
+Template: ensembl/port
+Default: 80
+Type: string
+Description: Port that Apache will listen on.
+
+Template: ensembl/webuserdbhost
+Default: localhost
+Type: string
+Description: MySQL server for web user db.
+
+Template: ensembl/webuserdbport
+Default: 3306
+Type: string
+Description: MySQL port for web user db.
+
+Template: ensembl/webuserdbname
+Default: ensembl
+Type: string
+Description: MySQL database name for web user db.
+
+Template: ensembl/webuserdbuser
+Default: ensembl
+Type: string
+Description: MySQL username for web user db.
+
+Template: ensembl/webuserdbpwd
+Default: ensembl
+Type: string
+Description: MySQL password for web user db.
+
+Template: ensembl/webuserdbexistyn
+Default: false
+Type: boolean
+Description: True if the web user db already exists.
+
+Template: ensembl/webuserdbkeepyn
+Default: true
+Type: boolean
+Description: True if the web user db already exists and should be kept.
+
+Template: ensembl/mysqladminuser
+Default: root
+Type: string
+Description: MySQL admin user for creating the web user db if it doesn't exist.
+
+Template: ensembl/mysqladminpwd
+Default: 
+Type: password
+Description: MySQL admin password for creating the web user db if it doesn't exist.
+
+Template: ensembl/webuserdbkeeptablesyn
+Default: true
+Type: boolean
+Description: True if the web user db already exists and the data in it should be kept.

Modified: trunk/packages/ensembl/ensembl/57/debian/init.d
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/init.d	2011-01-29 18:41:41 UTC (rev 5756)
+++ trunk/packages/ensembl/ensembl/57/debian/init.d	2011-01-29 18:53:10 UTC (rev 5757)
@@ -97,9 +97,6 @@
 		# 	chown nobody.nogroup "$d"
 		# 	chmod 755 "$d"
 		# done
-		ln -s /usr/share/ensembl/img-cache /var/cache/ensembl/img-cache
-		ln -s /usr/share/ensembl/img-tmp /var/tmp/ensembl/img-tmp
-		ln -s /usr/share/ensembl/tmp /var/tmp/ensembl/tmp
 
 		log_daemon_msg "Starting web server" "ensembl"
 		if $APACHE2CTL start; then

Modified: trunk/packages/ensembl/ensembl/57/debian/prepare_ensembl_source_packages.sh
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/prepare_ensembl_source_packages.sh	2011-01-29 18:41:41 UTC (rev 5756)
+++ trunk/packages/ensembl/ensembl/57/debian/prepare_ensembl_source_packages.sh	2011-01-29 18:53:10 UTC (rev 5757)
@@ -4,6 +4,7 @@
 
 startdir=`pwd`
 destdir=.
+ensemblversion=""
 
 
 if [ -d debian ]; then

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