@@ -169,10 +172,12 @@
check_table("uploads", $uploads_columns);
check_table("sharing", $sharing_columns);
+if($new==0) {
check_sessions();
check_uploads_ids();
check_all_files();
check_data_sources();
+}
fix_session_permissions();
fix_sqlite_permissions() if $type =~ /sqlite/i;
--- a/htdocs/index.html
+++ b/htdocs/index.html
@@ -24,7 +24,7 @@
/var/www/gbrowse2/example_scripts
-Example Databases
+Example Databases (requires gbrowse-data package)
@@ -32,9 +32,9 @@
installed for you. Try them at these URL:
@@ -56,13 +56,13 @@
http://your.host/gb2/gbrowse/yeast
http://your.host/gb2/gbrowse/yeast_advanced
http://your.host/gb2/gbrowse/yeast_renderfarm
-http://your.host/gb2/gbrowse/pop_demo (demo of embedded population allele frequency maps -- requires Template module to be installed)
Accelerated Demos
-If you have FastCGI and/or ModPerl installed, you will have access to
-an accelerated version of gbrowse at these URLs:
+By default, FastCGI and ModPerl are not set by gbrowse installation,
+However, if you have FastCGI and/or ModPerl installed, you will have access to
+ accelerated versions of gbrowse a these URLs:
- FastCGI
--- a/install_util/GBrowseInstall.pm
+++ b/install_util/GBrowseInstall.pm
@@ -33,6 +33,7 @@
wwwuser => 'User account under which Apache daemon runs?',
installconf => 'Automatically update Apache config files to run GBrowse?',
installetc => 'Automatically update system config files to run gbrowse-slave?',
+ registration_done => 'Set to 1 to skip registration.',
);
my %OK_PROPS = @OK_PROPS;
@@ -422,6 +423,82 @@
END
}
+sub ACTION_debianinstall {
+ my $self = shift;
+ my $prefix = $self->install_base || $self->prefix || 'debian/libgbrowse-perl';
+ GBrowseGuessDirectories->prefix($prefix);
+
+ $self->depends_on('config_data');
+
+ $self->install_path->{conf}
+ ||= $self->config_data('conf') || GBrowseGuessDirectories->conf;
+ $self->install_path->{htdocs}
+ ||= $self->config_data('htdocs')
+ || GBrowseGuessDirectories->htdocs;
+ $self->install_path->{'cgi-bin'}
+ ||= $self->config_data('cgibin')
+ || GBrowseGuessDirectories->cgibin;
+ $self->install_path->{'etc'}
+ ||= GBrowseGuessDirectories->etc;
+ $self->install_path->{'databases'}
+ ||= $self->config_data('databases')
+ || GBrowseGuessDirectories->databases;
+
+
+ $self->install_path->{conf} = $prefix.$self->install_path->{conf};
+ $self->install_path->{htdocs} = $prefix.$self->install_path->{htdocs};
+ $self->install_path->{'cgi-bin'} = $prefix.$self->install_path->{'cgi-bin'};
+ $self->install_path->{'etc'} = $prefix.$self->install_path->{'etc'};
+ $self->install_path->{'databases'} = $prefix.$self->install_path->{'databases'};
+ $self->SUPER::ACTION_install();
+
+ my $user = $self->config_data('wwwuser') || GBrowseGuessDirectories->wwwuser;
+
+ # fix some directories so that www user can write into them
+ my $tmp = $self->config_data('tmp') || GBrowseGuessDirectories->tmp;
+ $tmp = $prefix.$tmp;
+ mkpath($tmp);
+ my ($uid,$gid) = (getpwnam($user))[2,3];
+
+ # taint check issues
+ $uid =~ /^(\d+)$/;
+ $uid = $1;
+ $gid =~ /^(\d+)$/;
+ $gid = $1;
+
+ my $htdocs_i = File::Spec->catfile($self->install_path->{htdocs},'i');
+ my $images = File::Spec->catfile($tmp,'images');
+ my $htdocs = $self->install_path->{htdocs};
+ {
+ local $> = $uid;
+ symlink($images,$htdocs_i); # so symlinkifowner match works!
+ }
+
+ my $databases = $self->install_path->{'databases'};
+
+ #chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave');
+ #$self->fix_selinux;
+
+ my $base = basename($self->install_path->{htdocs});
+
+ # Configure the databases, if needed.
+ #print STDERR "Updating user account database...\n";
+ #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/var/lib/gbrowse/users.sqlite";
+
+}
+
+sub ACTION_debianinstall_slave {
+ my $self = shift;
+ my $prefix = $self->install_base || $self->prefix ||'';
+ GBrowseGuessDirectories->prefix($prefix);
+ $self->install_path->{'etc'} = $prefix.$self->install_path->{'etc'};
+ $self->SUPER::ACTION_install();
+}
+
+
sub ACTION_install {
my $self = shift;
my $prefix = $self->install_base || $self->prefix || '';
@@ -776,8 +853,9 @@
sub guess_user_account_db {
my $self = shift;
if (eval "require DBD::SQLite; 1") {
- my $databases = $self->config_data('databases');
- return "DBI:SQLite:$databases/users.sqlite";
+ #my $databases = $self->config_data('databases');
+ #return "DBI:SQLite:$databases/users.sqlite";
+ return "DBI:SQLite:/var/lib/gbrowse/users.sqlite";
} elsif (eval "require DBD::mysql; 1") {
return 'DBI:mysql:gbrowse_login;user=gbrowse;password=gbrowse';
} else {
--- a/conf/GBrowse.conf
+++ b/conf/GBrowse.conf
@@ -163,9 +163,9 @@
# "user_accounts" is true, then GBrowse
# will attempt to use its internal user accounts database
# to authenticate and/or register users.
-user_accounts = 1
-user_accounts_registration = 1
-user_accounts_openid = 1
+user_accounts = 0
+user_accounts_registration = 0
+user_accounts_openid = 0
# Path to the database -- you will need to create this database and grant all
# privileges on it to the indicated user.
debian/patches/skip_check_installed_test.patch 0000644 0000000 0000000 00000002320 12063031724 017032 0 ustar Author: Olivier Sallou
Subject: build steps checks for installed files
Description: For Debian program should not check
for installed files
Last-Updated: 2012-09-20
Forwarded: not-needed
--- a/install_util/GBrowseInstall.pm
+++ b/install_util/GBrowseInstall.pm
@@ -636,7 +636,7 @@
my $copied = $self->copy_if_modified($_=>'blib');
if ($copied || !$self->up_to_date('_build/config_data',"blib/$_")) {
$self->substitute_in_place("blib/$_");
- $self->check_installed($install_path,$base);
+ #$self->check_installed($install_path,$base);
}
}
@@ -698,7 +698,7 @@
my $copied = $self->copy_if_modified($base=>'blib');
if ($copied or !$self->up_to_date('_build/config_data',"blib/$base")) {
$self->substitute_in_place("blib/$base");
- $self->check_installed($install_path,$base) if $copied;
+ #$self->check_installed($install_path,$base) if $copied;
}
}
}
@@ -736,7 +736,7 @@
my $copied = $self->copy_if_modified($_=>'blib');
if ($copied or !$self->up_to_date('_build/config_data',"blib/$_")) {
$self->substitute_in_place("blib/$_");
- $self->check_installed($install_path,$base);
+ #$self->check_installed($install_path,$base);
}
}
}
debian/patches/skipRenderFarmTest_UpstreamBug12 0000644 0000000 0000000 00000002247 12063030200 016764 0 ustar Subject: remove renderfarm tests
Description: there is an upstream bug with renderfarm involved
tests. Upstream bug id 12 has been created witj instructions to
solve the issue. Runtime has been tested with no issue.
This patch remove tests using renderfarm feature.
Author: Olivier Sallou
Last-Updated: 2012-03-07
--- a/t/03.render.t
+++ b/t/03.render.t
@@ -16,9 +16,10 @@
use lib "$Bin/testdata";
use TemplateCopy; # for the template_copy() function
-use constant TEST_COUNT => 150;
+use constant TEST_COUNT => 0;
use constant CONF_FILE => "$Bin/testdata/conf/GBrowse.conf";
+exit 0;
my $PID;
BEGIN {
--- a/t/04.remoteserver.t
+++ b/t/04.remoteserver.t
@@ -12,10 +12,11 @@
use CGI;
use FindBin '$Bin';
-use constant TEST_COUNT => 47;
+use constant TEST_COUNT => 0;
use constant CONF_FILE => "$Bin/testdata/conf/GBrowse.conf";
use constant DEBUG => 0;
+exit 0;
my $PID;
BEGIN {
--- a/t/06.featuresearch.t
+++ b/t/06.featuresearch.t
@@ -11,9 +11,10 @@
use CGI;
use FindBin '$Bin';
-use constant TEST_COUNT => 26;
+use constant TEST_COUNT => 0;
use constant CONF_FILE => "$Bin/testdata/conf/GBrowse.conf";
+exit 0;
my $PID;
BEGIN {
debian/patches/fix_pop_url 0000644 0000000 0000000 00000003735 12063030200 013060 0 ustar Subject: update URL for default conf
Author: Olivier Sallou
Last-Update: 2011-08-08
Description: update URL for details in example conf files to match /gb2 instead of cgi-bin/gb2
Forwarded: not-needed
--- a/conf/yeast_chr1+2.conf
+++ b/conf/yeast_chr1+2.conf
@@ -158,7 +158,7 @@
This gene brought to you by SGD.
| Gene $name |
- | See gene details |
|---|
+ | See gene details |
|---|
| Ask SGD about $name |
|---|
| Ask Wikipedia about $name |
|---|
| Ask Google about $name |
|---|
--- a/conf/yeast_renderfarm.conf
+++ b/conf/yeast_renderfarm.conf
@@ -153,7 +153,7 @@
This gene brought to you by SGD.
Gene $name |
- | See gene details |
|---|
+ | See gene details |
|---|
| Ask SGD about $name |
|---|
| Ask Wikipedia about $name |
|---|
| Ask Google about $name |
|---|
debian/patches/gbrowse-slave-fix_defaults_path 0000644 0000000 0000000 00000001641 12063030200 016773 0 ustar Subject: fix default path on debian
Author: Olivier Sallou
Description: update path to be debian compliant, add description
Last-Updated: 2012-02-19
--- a/etc/init.d/gbrowse-slave
+++ b/etc/init.d/gbrowse-slave
@@ -1,11 +1,12 @@
#!/bin/sh
### BEGIN INIT INFO
-# Provides: gbrowse_slave
+# Provides: gbrowse-slave
# Required-Start: $remote_fs $syslog
# Required-Stop: $remote_fs $syslog
# Default-Start: 2 3 4 5
# Default-Stop: 0 1 6
# Short-Description: Start/Stop the gbrowse_slave rendering server.
+# Description: Enable the GBrowse slave rendering mode
### END INIT INFO
PATH=/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin
@@ -24,8 +25,8 @@
VERBOSITY=1
NICE=0
-if [ -f $ETC/default/gbrowse-slave ]; then
- . $ETC/default/gbrowse-slave
+if [ -f /etc/default/gbrowse-slave ]; then
+ . /etc/default/gbrowse-slave
fi
mkdir -p $RUNDIR
debian/patches/series 0000644 0000000 0000000 00000000223 12063030200 012011 0 ustar debian-packaging-patch
gbrowse-slave-fix_defaults_path
manpages.patch
fix_pop_url
skipRenderFarmTest_UpstreamBug12
skip_check_installed_test.patch
debian/patches/manpages.patch 0000644 0000000 0000000 00000012126 12063031672 013433 0 ustar Subject: fix POD-generated manual pages
Description: upstream pages contain errors
Author: Olivier Sallou
Last-Updated: 2012-09-25
Forwaded: yes
Bug: https://sourceforge.net/tracker/?func=detail&aid=3571433&group_id=27707&atid=391291
--- a/bin/gtf2gff3.pl
+++ b/bin/gtf2gff3.pl
@@ -1320,7 +1320,7 @@
=head1 NAME
-gtf2gff3
+gtf2gff3 - Converts GTF formatted files to valid GFF3 files
=head1 VERSION
@@ -1496,7 +1496,7 @@
=item C<< FATAL: Invalid value passed to strand: strand. >>
This may indicate that your GTF file does not indicate the strand for
-features that require it. Consider using the DEFAULT_STRAND paramater
+features that require it. Consider using the DEFAULT_STRAND parameter
in the config file. It may also indicate a software bug. Please
contact the author.
--- a/bin/wiggle2gff3.pl
+++ b/bin/wiggle2gff3.pl
@@ -2,7 +2,7 @@
=head1 NAME
-wiggle2gff3.pl
+wiggle2gff3.pl - Converts UCSC WIG format files into gff3 files
=head1 SYNOPSIS
--- a/lib/Bio/DB/GFF/Aggregator/match_gap.pm
+++ b/lib/Bio/DB/GFF/Aggregator/match_gap.pm
@@ -34,7 +34,6 @@
should be sufficient for simple nucleotide to nucleotide
alignments.
-################################################################################
=cut
--- a/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
+++ b/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
@@ -1,6 +1,6 @@
=head1 NAME
-package Bio::DB::GFF::Aggregator::reftranscript -- Aggregates references transcripts
+Bio::DB::GFF::Aggregator::reftranscript -- Aggregates references transcripts
=head1 SYNOPSIS
--- a/lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
+++ b/lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
@@ -23,7 +23,6 @@
=head2 METHODS
-=over 4
=cut
--- a/lib/Bio/Graphics/Browser2/DataBase.pm
+++ b/lib/Bio/Graphics/Browser2/DataBase.pm
@@ -66,12 +66,16 @@
$CACHE->delete($key);
}
+=over
+
=item Bio::Graphics::Browser2::DataBase->clone_databases()
Call this after a fork in the child process to make sure that all open
databases have had a chance to clone themselves if they need
to. Otherwise you will get random database failures.
+=back
+
=cut
sub clone_databases {
--- a/lib/Bio/Graphics/Browser2/Plugin.pm
+++ b/lib/Bio/Graphics/Browser2/Plugin.pm
@@ -238,7 +238,7 @@
The purpose of this methods is to suppress the 'Configure...'
or 'Find...' title that is printed at the top of the page when the
-plugin is loaded. It will return false unless overriden by a plugin where
+plugin is loaded. It will return false unless overridden by a plugin where
this behaviour is desired.
=item $type = $self->type()
--- a/lib/Bio/Graphics/Browser2/Region.pm
+++ b/lib/Bio/Graphics/Browser2/Region.pm
@@ -3,6 +3,12 @@
# provide method for fetching and manipulating the current
# region or regions.
+=head1 NAME
+
+Bio::Graphics::Browser2::Region -- Provide method for fetching and manipulating regions
+
+=cut
+
use strict;
use warnings;
use Bio::Graphics::Browser2::Shellwords;
--- a/lib/Bio/Graphics/Browser2/Render.pm
+++ b/lib/Bio/Graphics/Browser2/Render.pm
@@ -3,6 +3,12 @@
use strict;
use warnings;
+=head1 NAME
+
+Bio::Graphics::Browser2::Render -- Provide methods to render regions
+
+=cut
+
use JSON;
use Digest::MD5 'md5_hex';
use CGI qw(:standard param request_method header url iframe img span div br center url_param);
--- a/lib/Bio/Graphics/Browser2/RenderPanels.pm
+++ b/lib/Bio/Graphics/Browser2/RenderPanels.pm
@@ -2,6 +2,13 @@
use strict;
use warnings;
+=head1 NAME
+
+Bio::Graphics::Browser2::RenderPanels-- Provide methods to render a panel
+
+=cut
+
+
use GD 'gdTransparent','gdStyled';
use Bio::Graphics;
--- a/lib/Legacy/Graphics/Browser.pm
+++ b/lib/Legacy/Graphics/Browser.pm
@@ -4,6 +4,12 @@
# This is an old version of Bio::Graphics::Browser retained for gbrowse_syn
# It is on the path to deprecation
+=head1 NAME
+
+Legacy::Graphics::Browser-- Old version, deprecated
+
+=cut
+
=head1 METHODS
The remainder of this document describes the methods available to the
--- a/lib/Bio/Graphics/Browser2/DataSource.pm
+++ b/lib/Bio/Graphics/Browser2/DataSource.pm
@@ -32,6 +32,10 @@
}
}
+=head1 NAME
+
+Bio::Graphics::Browser2::DataSource -- DataSource to access data
+
=head1 SYNOPSIS
=head1 DESCRIPTION
@@ -150,6 +154,8 @@
delete $CONFIG_CACHE{$self->config_file};
}
+
+=back
=head2 userdata()
$path = $source->userdata(@path_components)
@@ -871,6 +877,8 @@
croak "Do not call make_link() on the DataSource. Call it on the Render object";
}
+=over
+
=item $db = $dsn->databases
Return all named databases from [name:database] tracks.
@@ -1116,6 +1124,8 @@
%DB_SETTINGS = ();
}
+=back
+
=head2 generate_image
($url,$path) = generate_image($gd);
--- a/bin/gbrowse_grow_cloud_vol.pl
+++ b/bin/gbrowse_grow_cloud_vol.pl
@@ -2,13 +2,13 @@
=head1 NAME
-gbrowse_grow_cloud-vol.pl Grow the GBrowse volume by the requested amount
+gbrowse_grow_cloud-vol \- Grow the GBrowse volume by the requested amount
=head1 SYNOPSYS
Grow /opt/gbrowse by another 100 gigabytes
- % gbrowse_grow_cloud_vol.pl 100
+ % gbrowse_grow_cloud_vol 100
=head1 DESCRIPTION
debian/gbrowse_import_ucsc_db.1 0000644 0000000 0000000 00000002431 12063030200 013756 0 ustar .TH GBrowse2 1 "February 07, 2011" "version 1.1.0" "USER COMMANDS"
.SH NAME
browse_import_ucsc_db \- Creates a framework data source
.SH DESCRIPTION
This creates a framework data source for one of the genomes known to
the UCSC Genome Browser. You can then modify the data source
configuration file, add your own data, and so forth. Provide the name
of a UCSC genome build and optionally a description to display in
GBrowse.
To get started, find the desired data source by going to
http://genome.ucsc.edu/cgi-bin/hgGateway and using the "clade" and
"genome" menus to navigate to the desired species and build
number. You will find the data source name in the blue box below the
navigation controls. Look for something like this:
D. melanogaster Genome Browser – dm3 assembly (sequences)
The data source name appears before the word "assembly", in this case
"dm3".
.SH USAGE
[options] []
.SH OPTIONS
To get a list of all sources recognized by UCSC appears type:
browse_import_ucsc_db \-\-list
Options:
\-\-remove-chr Remove the 'chr' prefix from all chromosome names
\-\-list List data sources
.SH EXAMPLE
Example: $0 hg19 'Human genome (hg19)'
.SH AUTHOR
Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging
Lincoln Stein - GBrowse
debian/compat 0000644 0000000 0000000 00000000002 11720205701 010357 0 ustar 8
debian/control 0000644 0000000 0000000 00000005642 12152113130 010565 0 ustar Source: gbrowse
Section: science
Priority: optional
Build-Depends: bioperl (>= 1.6.901), debhelper (>= 9), dh-apache2,
libbio-graphics-perl (>= 2.31),
libcapture-tiny-perl,
libcgi-session-perl (>= 4.02),
libgd-gd2-perl (>= 2.07) | libgd-gd2-noxpm-perl (>= 2.07),
libio-string-perl,
libjson-perl,
libstatistics-descriptive-perl,
libwww-perl,
libhttp-daemon-perl, perl,
perl (>= 5.10.0) | libextutils-cbuilder-perl,
sqlite3, libdbd-sqlite3-perl,
libterm-readkey-perl,
libjs-prototype (>=1.7), libjs-scriptaculous (>= 1.9),
libvm-ec2-perl
Maintainer: Debian Med Packaging Team
Uploaders: Olivier Sallou ,
Charles Plessy , Aaron M. Ucko
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/gmod/gbrowse/trunk/
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/gmod/gbrowse/
Standards-Version: 3.9.3
Homepage: http://www.gbrowse.org/
Package: gbrowse
Architecture: all
Depends: ${misc:Depends}, ${perl:Depends},
apache2 (>= 2.4) | httpd-cgi,
bioperl (>= 1.6.901), libbio-graphics-perl (>= 2.31),
libcgi-session-perl (>= 4.02),
libgd-gd2-noxpm-perl (>= 2.07) | libgd-gd2-perl (>= 2.07),
libio-string-perl,
libjson-perl,
libstatistics-descriptive-perl,
libwww-perl,
libhttp-daemon-perl,
perl (>= 5.10.0) | libextutils-cbuilder-perl,
libterm-readkey-perl,
sqlite3, libdbd-sqlite3-perl,
libjs-prototype (>=1.7), libjs-scriptaculous (>=1.9),
libvm-ec2-perl
Recommends: ${misc:Recommends}
Suggests: gbrowse-data, gbrowse-calign, libfile-nfslock-perl
Description: GMOD Generic Genome Browser
Generic Genome Browser is a simple but highly
configurable web-based genome browser. It is a component of the
Generic Model Organism Systems Database project (GMOD).
Some of its features:
* Simultaneous bird's eye and detailed views of the genome;
* Scroll, zoom, center;
* Attach arbitrary URLs to any annotation;
* Order and appearance of tracks are customizable by administrator and
end-user;
* Search by annotation ID, name, or comment;
* Supports third party annotation using GFF formats;
* Settings persist across sessions;
* DNA and GFF dumps;
* Connectivity to different databases, including BioSQL and Chado;
* Multi-language support;
* Third-party feature loading;
* Customizable plug-in architecture (e.g. run BLAST, dump & import many
formats, find oligonucleotides, design primers, create restriction maps,
edit features).
Package: gbrowse-data
Architecture: all
Depends: ${misc:Depends}
Recommends: gbrowse
Description: Sample data to use GBrowse
This package contains sample data to test the gbrowse tool
with the Yeast genome.
Package: gbrowse-calign
Architecture: any
Depends: ${perl:Depends},${shlibs:Depends},${misc:Depends}, perl (>= 5.10.0), gbrowse
Description: CAlign helper
This package provides the CAlign helper
for use with Realign. It speeds up Smith-Waterman alignment.
debian/postinst 0000644 0000000 0000000 00000001255 11720664455 011011 0 ustar #!/bin/bash
set -e
case "$1" in
configure)
if [ ! -d /var/cache/gbrowse ] ; then
mkdir -p /var/cache/gbrowse
fi
chown -R root:www-data /var/lib/gbrowse
chmod -R 770 /var/lib/gbrowse
chown -R root:www-data /var/cache/gbrowse
chmod -R 770 /var/cache/gbrowse
if [ -e /var/cache/gbrowse/sessions ]; then
chown -R www-data:www-data /var/cache/gbrowse/sessions
fi
update-rc.d gbrowse-slave defaults > /dev/null
;;
abort-upgrade|abort-remove|abort-deconfigure)
;;
*)
echo "postinst called with unknown argument \`$1'" >&2
exit 1
;;
esac
#DEBHELPER#
debian/gbrowse-data.postinst 0000644 0000000 0000000 00000000642 11720205701 013347 0 ustar #!/bin/bash
set -e
case "$1" in
configure)
chown -R root:www-data /var/lib/gbrowse/databases
chmod -R 770 /var/lib/gbrowse/databases
if [ -e /etc/init.d/gbrowse-slave ] ; then
invoke-rc.d gbrowse-slave restart
fi
;;
abort-upgrade|abort-remove|abort-deconfigure)
;;
*)
echo "postinst called with unknown argument \`$1'" >&2
exit 1
;;
esac
#DEBHELPER#
debian/changelog 0000644 0000000 0000000 00000005321 12231465203 011037 0 ustar gbrowse (2.54+dfsg-2build1) trusty; urgency=low
* Rebuild for Perl 5.18.
-- Colin Watson Tue, 22 Oct 2013 13:07:30 +0100
gbrowse (2.54+dfsg-2) unstable; urgency=low
* Transition to apache 2.4 (Closes: #669830).
-- Olivier Sallou Sat, 25 May 2013 11:46:26 +0200
gbrowse (2.54+dfsg-1) unstable; urgency=low
* New upstream release
* debian/control: increase min bio-graphics version
-- Olivier Sallou Sat, 15 Dec 2012 09:11:03 +0100
gbrowse (2.51+dfsg-1) unstable; urgency=low
[ Olivier Sallou ]
* new upstream release (Closes: #677381).
* fixes make test issue and plugins impact (Closes: #662922).
* debian/control: switch to Standards 3.9.3
[ Andreas Tille ]
* debian/upstream: Added citation information
-- Olivier Sallou Wed, 07 Mar 2012 10:36:52 +0100
gbrowse (2.48~dfsg-1) unstable; urgency=low
[ Olivier Sallou ]
* new upstream release
* debian/control: add libbiographics-perl dependency
* debian/patches/skipRenderFarmTest_UpstreamBug12: fix an upstream
test issue on renderfarm testing.
[ Charles Plessy ]
* Updated VCS URLs (debian/control).
-- Olivier Sallou Sun, 19 Feb 2012 15:59:53 +0100
gbrowse (2.42~dfsg-1) unstable; urgency=low
* New upstream release
-- Olivier Sallou Tue, 18 Oct 2011 15:37:42 +0200
gbrowse (2.39~dfsg-2) unstable; urgency=low
* Skip deferred rendering tests causing random failures on build servers
-- Olivier Sallou Mon, 29 Aug 2011 10:34:12 -0400
gbrowse (2.39~dfsg-1) unstable; urgency=low
* New upstream version
-- Olivier Sallou Mon, 8 Aug 2011 10:34:12 -0400
gbrowse (2.38~dfsg-1) unstable; urgency=low
* New upstream version
* New patch to fix gbrowse-slace defaults script
-- Olivier Sallou Sat, 18 Jun 2011 13:55:12 -0400
gbrowse (2.26~dfsg-3) unstable; urgency=low
* Bump version to compensate for botched uploads of -2. (It's been a
long day.)
-- Aaron M. Ucko Tue, 26 Apr 2011 22:55:12 -0400
gbrowse (2.26~dfsg-2) unstable; urgency=low
* Team upload.
* Upload to unstable, where -1 accidentally landed.
* debian/{gbrowse.dirs,rules}: Tweak to avoid errors when building just
the architecture-dependent gbrowse-calign package. (Closes: #624130.)
* debian/control: Temporarily add myself to uploaders to placate dak.
-- Aaron M. Ucko Tue, 26 Apr 2011 21:46:23 -0400
gbrowse (2.26~dfsg-1) experimental; urgency=low
[ Olivier Sallou ]
* Initial Release (Closes: #429610).
-- Charles Plessy Wed, 13 Apr 2011 14:45:45 +0900