[med-svn] r5854 - in trunk/packages/ensembl/ensembl/57/debian: . po
Steffen Möller
moeller at alioth.debian.org
Wed Feb 2 12:12:55 UTC 2011
Author: moeller
Date: 2011-02-02 12:12:35 +0000 (Wed, 02 Feb 2011)
New Revision: 5854
Removed:
trunk/packages/ensembl/ensembl/57/debian/ensembl.default.ex
Modified:
trunk/packages/ensembl/ensembl/57/debian/control
trunk/packages/ensembl/ensembl/57/debian/ensembl.postinst
trunk/packages/ensembl/ensembl/57/debian/ensembl.templates
trunk/packages/ensembl/ensembl/57/debian/po/templates.pot
trunk/packages/ensembl/ensembl/57/debian/rules
Log:
Upload of version 57-5
Modified: trunk/packages/ensembl/ensembl/57/debian/control
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/control 2011-02-02 08:57:13 UTC (rev 5853)
+++ trunk/packages/ensembl/ensembl/57/debian/control 2011-02-02 12:12:35 UTC (rev 5854)
@@ -4,7 +4,7 @@
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
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: debhelper (>= 7.0.50~), po-debconf
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
@@ -16,6 +16,7 @@
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
+Section: science
Description: Installs a basic Ensembl 57 genome browser.
Ensembl is a joint project of the Sanger Center and the European
Bioinformatics Institute, an outstation of the European Molecular
@@ -57,6 +58,7 @@
Architecture: all
Depends: ${misc:Depends},bioperl1.2.3|bioperl
Suggests: ksh | mksh | pdksh | zsh, tk
+Section: perl
Description: core libraries of Ensembl API
The Ensembl project presents the sequence data for the yet
available complete genomes of many vertebrates and is helped by many
@@ -75,6 +77,7 @@
Package: libensembl-functgenomics-perl
Depends: ${misc:Depends},libensembl-core-perl
Architecture: all
+Section: perl
Description: API for functional genomics with Ensembl
The Ensembl project presents the sequence data for the yet
available complete genomes of many vertebrates and is helped by many
@@ -87,6 +90,7 @@
Package: libensembl-compara-perl
Depends: ${misc:Depends},libensembl-core-perl
Architecture: all
+Section: perl
Description: API for comparative genomics with Ensembl
The Ensembl project presents the sequence data for the yet
available complete genomes of many vertebrates and is helped by many
@@ -104,6 +108,7 @@
Package: libensembl-external-perl
Depends: ${misc:Depends},libensembl-core-perl
Architecture: all
+Section: perl
Description: API for integration of external data sources with Ensembl
The Ensembl project presents the sequence data for the yet
available complete genomes of many vertebrates and is helped by many
@@ -117,6 +122,7 @@
Package: libensembl-variation-perl
Depends: ${misc:Depends},libensembl-core-perl
Architecture: all
+Section: perl
Description: Ensembl API for investigation of inter-individual genomic differences
The Ensembl project presents the sequence data for the yet
available complete genomes of many vertebrates and is helped by many
@@ -132,6 +138,7 @@
Package: libensembl-draw-perl
Depends: ${misc:Depends},libensembl-core-perl
Architecture: all
+Section: perl
Description: Ensembl API for graphical representation of genomic properties
The Ensembl project presents the sequence data for the yet
available complete genomes of many vertebrates and is helped by many
@@ -143,6 +150,7 @@
Package: ensembl-bin
Depends: ${shlibs:Depends}, ${misc:Depends}
Architecture: any
+Section: utils
Description: platform-specific files of Ensembl
The Ensembl website is mostly implemented in Perl. But just a few
bits do appear as binaries. Those are gathered in this package.
Deleted: trunk/packages/ensembl/ensembl/57/debian/ensembl.default.ex
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/ensembl.default.ex 2011-02-02 08:57:13 UTC (rev 5853)
+++ trunk/packages/ensembl/ensembl/57/debian/ensembl.default.ex 2011-02-02 12:12:35 UTC (rev 5854)
@@ -1,10 +0,0 @@
-# Defaults for ensembl initscript
-# sourced by /etc/init.d/ensembl
-# installed at /etc/default/ensembl by the maintainer scripts
-
-#
-# This is a POSIX shell fragment
-#
-
-# Additional options that are passed to the Daemon.
-DAEMON_OPTS=""
Modified: trunk/packages/ensembl/ensembl/57/debian/ensembl.postinst
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/ensembl.postinst 2011-02-02 08:57:13 UTC (rev 5853)
+++ trunk/packages/ensembl/ensembl/57/debian/ensembl.postinst 2011-02-02 12:12:35 UTC (rev 5854)
@@ -134,5 +134,4 @@
fi
# End automatically added section
-
exit 0
Modified: trunk/packages/ensembl/ensembl/57/debian/ensembl.templates
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/ensembl.templates 2011-02-02 08:57:13 UTC (rev 5853)
+++ trunk/packages/ensembl/ensembl/57/debian/ensembl.templates 2011-02-02 12:12:35 UTC (rev 5854)
@@ -1,90 +1,159 @@
Template: ensembl/port
-Default: 80
+Default: 8000
Type: string
_Description: Port that Apache will listen on:
- Ensembl presents itself to the user via
- a web server. When there are multiple
- web pages on the same server, it is not
- unlikely that Ensembl should have a different
- than the default port 80.
+ The Ensembl web interface runs apache underneath. If no other service is
+ running on the same machine, the port should most likely be 80, just as
+ with regular web services. We presume another web server and/or tomcat
+ (8080) to be already running and have chosen port 8000 as a default.
+
Template: ensembl/webuserdbhost
Default: localhost
Type: string
_Description: MySQL server for web user db:
- The local installation of Ensembl needs a
- MySQL Database server to store user-associated
- data. Please specify the hostname of the
- server here. Enter it in the same way
- that you would use to log into that machine
- when using it manually from the server and
- test that you have all the right access
- permissions.
+ The Ensembl web interface has the option to store temporary data locally,
+ so it does not need to transfer all information all the time from one
+ web page to another but has those readily available in a database.
+ .
+ Please specify the IP number or hostname of the server here. Enter
+ it in the same way that you would use to log into that machine when
+ using it manually from the server and test that you have all the right
+ access permissions.
+
Template: ensembl/webuserdbport
Default: 3306
Type: string
_Description: MySQL port for web user db:
- The port of the local MySQL database.
+ The Ensembl web interface has the option to store temporary
+ data locally, so it does not need to transfer all information
+ all the time from one web page to another but has those readily
+ available in a database.
+ .
+ For most installations, this database will be MySQL,
+ which by default listens to port 3306. This may be different
+ if that machine has another instance of MySQL already.
+
Template: ensembl/webuserdbname
Default: ensembl
Type: string
_Description: MySQL database name for web user db:
- The local database to store user associated
- data for Ensembl shall have a name.
+ The Ensembl web interface has the option to store temporary
+ data locally, so it does not need to transfer all information
+ all the time from one web page to another but has those readily
+ available in a database.
+ .
+ If you change this name to something else than the default,
+ then you must be a real advanced user and do not need any
+ further description ob what this thing is doing.
+
Template: ensembl/webuserdbuser
Default: ensembl
Type: string
_Description: MySQL username for web user db:
- The username under which the database can be
- accessed.
+ The Ensembl web interface has the option to store temporary data locally,
+ so it does not need to transfer all information all the time from one
+ web page to another but has those readily available in a database.
+ .
+ This parameter sets the username under which the database can be
+ accessed. Security sensitive admins may decide to specify a database
+ user for the local database that differs from the default. But the
+ Ensembl installation is complex, i.e. you may into unexpected issues when
+ diverging from the default.
+ .
+ Please start with the default as a start. To increase security, allow
+ access only from the machine that runs the web server.
+
Template: ensembl/webuserdbpwd
Default: ensembl
Type: string
_Description: MySQL password for web user db:
- The password with which to access the local
- Ensembl database.
+ The Ensembl web interface has the option to store temporary
+ data locally, so it does not need to transfer all information
+ all the time from one web page to another but has those readily
+ available in a database.
+ .
+ Security sensitive admins may decide to specify a password for
+ that database' user that differs from the default. But the Ensembl
+ installation is complex, i.e. you may into unexpected issues when
+ diverging from the default.
+ .
+ Please start with the default as a start. To increase security, allow
+ access only from the machine that runs the web server.
+
Template: ensembl/webuserdbexistyn
Default: false
Type: boolean
_Description: Does web user db already exist?
- When installing Ensembl, the local database may
- already exist, e.g. from a previous installation.
+ The Ensembl web interface has the option to store temporary
+ data locally, so it does not need to transfer all information
+ all the time from one web page to another but has those readily
+ available in a database.
.
- True if the web user db already exists.
+ Please specify with 'Y' if the database does already exist. If
+ you answer with 'N', it will be created for you. If 'Y', you
+ will be asked if the existing data should be overwritten.
+
Template: ensembl/webuserdbkeepyn
Default: true
Type: boolean
_Description: If existing, should the web user db be kept?
+ The Ensembl web interface has the option to store temporary
+ data locally, so it does not need to transfer all information
+ all the time from one web page to another but has those readily
+ available in a database.
+ .
When there is a previous installation of the local
database to support the web interface, one may argue if that
should be overridden during an update.
.
- True if the web user db already exists and should be kept:
+ Anser with 'Y' if the previous data should be kept. This only
+ works when there are no changes done to the database schema.
+ If not sure, answer 'N'.
+
Template: ensembl/mysqladminuser
Default: root
Type: string
_Description: MySQL admin user for creating the web user db if it doesn't exist:
- When a new database shall be created, one needs a user with the
- permissions to perform so.
+ The Ensembl web interface has the option to store temporary
+ data locally, so it does not need to transfer all information
+ all the time from one web page to another but has those readily
+ available in a database.
+ .
+ To create the database you need special permissions that
+ this admin user shall have.
+ .
+ This parameter is only required if the user database does not yet exist
+ or it was previously opted that this shall be created again.
Template: ensembl/mysqladminpwd
Default:
Type: password
_Description: MySQL admin password for creating the web user db if it doesn't exist:
- The user with the right to create a new database most likely has a password.
+ The Ensembl web interface has the option to store temporary
+ data locally, so it does not need to transfer all information
+ all the time from one web page to another but has those readily
+ available in a database.
+ .
+ This specifies the password with which the admin user can
+ access the database.
+ .
+ This parameter is only required if the user database does not yet exist
+ or it was previously opted that this shall be created again.
Template: ensembl/webuserdbkeeptablesyn
Default: true
Type: boolean
_Description: Shall the data in web user db be kept by package update?
- When the database is available, the remaining question is how to perform with
- already existing tables.
+ Keeping the web user database means you don't have to recreate
+ it, but you might want to drop and recreate the tables within it.
.
- True if the web user db already exists and the data in it should be kept:
+ If you didn't keep the database, you don't need to answer this.
+ If the database didn't already exist, you don't need to answer.
Modified: trunk/packages/ensembl/ensembl/57/debian/po/templates.pot
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/po/templates.pot 2011-02-02 08:57:13 UTC (rev 5853)
+++ trunk/packages/ensembl/ensembl/57/debian/po/templates.pot 2011-02-02 12:12:35 UTC (rev 5854)
@@ -8,7 +8,7 @@
msgstr ""
"Project-Id-Version: PACKAGE VERSION\n"
"Report-Msgid-Bugs-To: ensembl at packages.debian.org\n"
-"POT-Creation-Date: 2011-01-29 22:38+0100\n"
+"POT-Creation-Date: 2011-02-02 00:07+0100\n"
"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
"Last-Translator: FULL NAME <EMAIL at ADDRESS>\n"
"Language-Team: LANGUAGE <LL at li.org>\n"
@@ -20,66 +20,169 @@
#. Type: string
#. Description
#: ../ensembl.templates:1001
-msgid "Port that Apache will listen on."
+msgid "Port that Apache will listen on:"
msgstr ""
#. Type: string
#. Description
+#: ../ensembl.templates:1001
+msgid ""
+"Ensembl presents itself to the user via a web server. When there are "
+"multiple web pages on the same server, it is not unlikely that Ensembl "
+"should have a different than the default port 80."
+msgstr ""
+
+#. Type: string
+#. Description
#: ../ensembl.templates:2001
-msgid "MySQL server for web user db."
+msgid "MySQL server for web user db:"
msgstr ""
#. Type: string
#. Description
+#: ../ensembl.templates:2001
+msgid ""
+"The local installation of Ensembl needs a MySQL Database server to store "
+"user-associated data. Please specify the hostname of the server here. Enter "
+"it in the same way that you would use to log into that machine when using it "
+"manually from the server and test that you have all the right access "
+"permissions."
+msgstr ""
+
+#. Type: string
+#. Description
#: ../ensembl.templates:3001
-msgid "MySQL port for web user db."
+msgid "MySQL port for web user db:"
msgstr ""
#. Type: string
#. Description
+#: ../ensembl.templates:3001
+msgid "The port of the local MySQL database."
+msgstr ""
+
+#. Type: string
+#. Description
#: ../ensembl.templates:4001
-msgid "MySQL database name for web user db."
+msgid "MySQL database name for web user db:"
msgstr ""
#. Type: string
#. Description
+#: ../ensembl.templates:4001
+msgid ""
+"The local database to store user associated data for Ensembl shall have a "
+"name."
+msgstr ""
+
+#. Type: string
+#. Description
#: ../ensembl.templates:5001
-msgid "MySQL username for web user db."
+msgid "MySQL username for web user db:"
msgstr ""
#. Type: string
#. Description
+#: ../ensembl.templates:5001
+msgid "The username under which the database can be accessed."
+msgstr ""
+
+#. Type: string
+#. Description
#: ../ensembl.templates:6001
-msgid "MySQL password for web user db."
+msgid "MySQL password for web user db:"
msgstr ""
+#. Type: string
+#. Description
+#: ../ensembl.templates:6001
+msgid "The password with which to access the local Ensembl database."
+msgstr ""
+
#. Type: boolean
#. Description
#: ../ensembl.templates:7001
+msgid "Does web user db already exist?"
+msgstr ""
+
+#. Type: boolean
+#. Description
+#: ../ensembl.templates:7001
+msgid ""
+"When installing Ensembl, the local database may already exist, e.g. from a "
+"previous installation."
+msgstr ""
+
+#. Type: boolean
+#. Description
+#: ../ensembl.templates:7001
msgid "True if the web user db already exists."
msgstr ""
#. Type: boolean
#. Description
#: ../ensembl.templates:8001
-msgid "True if the web user db already exists and should be kept."
+msgid "If existing, should the web user db be kept?"
msgstr ""
+#. Type: boolean
+#. Description
+#: ../ensembl.templates:8001
+msgid ""
+"When there is a previous installation of the local database to support the "
+"web interface, one may argue if that should be overridden during an update."
+msgstr ""
+
+#. Type: boolean
+#. Description
+#: ../ensembl.templates:8001
+msgid "True if the web user db already exists and should be kept:"
+msgstr ""
+
#. Type: string
#. Description
#: ../ensembl.templates:9001
-msgid "MySQL admin user for creating the web user db if it doesn't exist."
+msgid "MySQL admin user for creating the web user db if it doesn't exist:"
msgstr ""
+#. Type: string
+#. Description
+#: ../ensembl.templates:9001
+msgid ""
+"When a new database shall be created, one needs a user with the permissions "
+"to perform so."
+msgstr ""
+
#. Type: password
#. Description
#: ../ensembl.templates:10001
-msgid "MySQL admin password for creating the web user db if it doesn't exist."
+msgid "MySQL admin password for creating the web user db if it doesn't exist:"
msgstr ""
+#. Type: password
+#. Description
+#: ../ensembl.templates:10001
+msgid ""
+"The user with the right to create a new database most likely has a password."
+msgstr ""
+
#. Type: boolean
#. Description
#: ../ensembl.templates:11001
+msgid "Shall the data in web user db be kept by package update?"
+msgstr ""
+
+#. Type: boolean
+#. Description
+#: ../ensembl.templates:11001
msgid ""
-"True if the web user db already exists and the data in it should be kept."
+"When the database is available, the remaining question is how to perform "
+"with already existing tables."
msgstr ""
+
+#. Type: boolean
+#. Description
+#: ../ensembl.templates:11001
+msgid ""
+"True if the web user db already exists and the data in it should be kept:"
+msgstr ""
Modified: trunk/packages/ensembl/ensembl/57/debian/rules
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/rules 2011-02-02 08:57:13 UTC (rev 5853)
+++ trunk/packages/ensembl/ensembl/57/debian/rules 2011-02-02 12:12:35 UTC (rev 5854)
@@ -133,6 +133,7 @@
clean:
rm -f ensembl-variation/C_code/calc_genotypes.o ensembl-variation/C_code/calc_genotypes
+ debconf-updatepo
dh_clean install-indep-paths install-indep-copying \
build-stamp build-indep-stamp build-arch-stamp \
configure-stamp
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