[med-svn] r12287 - in trunk/packages/gmod/gbrowse/tags: . 2.51+dfsg-1/debian 2.51+dfsg-1/debian/patches
Olivier Sallou
osallou at alioth.debian.org
Tue Sep 25 07:54:53 UTC 2012
Author: osallou
Date: 2012-09-25 07:54:53 +0000 (Tue, 25 Sep 2012)
New Revision: 12287
Added:
trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/
trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/changelog
trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/control
trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/debian-packaging-patch
trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/fix_pop_url
trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/gbrowse-slave-fix_defaults_path
trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/manpages.patch
trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/skipRenderFarmTest_UpstreamBug12
trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/skip_check_installed_test.patch
Removed:
trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/changelog
trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/control
trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/debian-packaging-patch
trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/fix_pop_url
trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/gbrowse-slave-fix_defaults_path
trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/manpages.patch
trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/skipRenderFarmTest_UpstreamBug12
trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/skip_check_installed_test.patch
Log:
[svn-buildpackage] Tagging gbrowse 2.51+dfsg-1
Deleted: trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/changelog
===================================================================
--- trunk/packages/gmod/gbrowse/trunk/debian/changelog 2012-09-25 07:07:28 UTC (rev 12281)
+++ trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/changelog 2012-09-25 07:54:53 UTC (rev 12287)
@@ -1,74 +0,0 @@
-gbrowse (2.51~dfsg-1) UNRELEASED; urgency=low
-
- [ Olivier Sallou ]
- * new upstream release (Closes: #677381).
- * fixes make test issue and plugins impact (Closes: #662922).
- * NOT RELEASED YET, needs libvm-ec2-perl
-
- [ Andreas Tille ]
- * debian/upstream: Added citation information
-
- -- Olivier Sallou <osallou at debian.org> 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 <olivier.sallou at irisa.fr> Sun, 19 Feb 2012 15:59:53 +0100
-
-gbrowse (2.42~dfsg-1) unstable; urgency=low
-
- * New upstream release
-
- -- Olivier Sallou <olivier.sallou at irisa.fr> 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 <olivier.sallou at irisa.fr> Mon, 29 Aug 2011 10:34:12 -0400
-
-
-gbrowse (2.39~dfsg-1) unstable; urgency=low
-
- * New upstream version
-
- -- Olivier Sallou <olivier.sallou at irisa.fr> 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 <olivier.sallou at irisa.fr> 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 <ucko at debian.org> 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 <ucko at debian.org> Tue, 26 Apr 2011 21:46:23 -0400
-
-gbrowse (2.26~dfsg-1) experimental; urgency=low
-
- [ Olivier Sallou ]
- * Initial Release (Closes: #429610).
-
- -- Charles Plessy <plessy at debian.org> Wed, 13 Apr 2011 14:45:45 +0900
Copied: trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/changelog (from rev 12286, trunk/packages/gmod/gbrowse/trunk/debian/changelog)
===================================================================
--- trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/changelog (rev 0)
+++ trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/changelog 2012-09-25 07:54:53 UTC (rev 12287)
@@ -0,0 +1,74 @@
+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 <osallou at debian.org> 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 <olivier.sallou at irisa.fr> Sun, 19 Feb 2012 15:59:53 +0100
+
+gbrowse (2.42~dfsg-1) unstable; urgency=low
+
+ * New upstream release
+
+ -- Olivier Sallou <olivier.sallou at irisa.fr> 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 <olivier.sallou at irisa.fr> Mon, 29 Aug 2011 10:34:12 -0400
+
+
+gbrowse (2.39~dfsg-1) unstable; urgency=low
+
+ * New upstream version
+
+ -- Olivier Sallou <olivier.sallou at irisa.fr> 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 <olivier.sallou at irisa.fr> 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 <ucko at debian.org> 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 <ucko at debian.org> Tue, 26 Apr 2011 21:46:23 -0400
+
+gbrowse (2.26~dfsg-1) experimental; urgency=low
+
+ [ Olivier Sallou ]
+ * Initial Release (Closes: #429610).
+
+ -- Charles Plessy <plessy at debian.org> Wed, 13 Apr 2011 14:45:45 +0900
Deleted: trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/control
===================================================================
--- trunk/packages/gmod/gbrowse/trunk/debian/control 2012-09-25 07:07:28 UTC (rev 12281)
+++ trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/control 2012-09-25 07:54:53 UTC (rev 12287)
@@ -1,63 +0,0 @@
-Source: gbrowse
-Section: science
-Priority: optional
-Build-Depends: bioperl (>= 1.6.901), debhelper (>= 8),
- libbio-graphics-perl (>= 2.28), 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 <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Olivier Sallou <osallou at debian.org>,
- Charles Plessy <plessy at debian.org>, Aaron M. Ucko <ucko at debian.org>
-DM-Upload-Allowed: yes
-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: 3.9.2
-Homepage: http://www.gbrowse.org/
-
-Package: gbrowse
-Architecture: all
-Depends: ${misc:Depends}, ${perl:Depends},
- bioperl (>= 1.6.901), libbio-graphics-perl (>= 2.28),
- 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,
- 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
-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.
Copied: trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/control (from rev 12285, trunk/packages/gmod/gbrowse/trunk/debian/control)
===================================================================
--- trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/control (rev 0)
+++ trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/control 2012-09-25 07:54:53 UTC (rev 12287)
@@ -0,0 +1,63 @@
+Source: gbrowse
+Section: science
+Priority: optional
+Build-Depends: bioperl (>= 1.6.901), debhelper (>= 8),
+ libbio-graphics-perl (>= 2.28), 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 <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Olivier Sallou <osallou at debian.org>,
+ Charles Plessy <plessy at debian.org>, Aaron M. Ucko <ucko at debian.org>
+DM-Upload-Allowed: yes
+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},
+ bioperl (>= 1.6.901), libbio-graphics-perl (>= 2.28),
+ 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,
+ 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
+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.
Deleted: trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/debian-packaging-patch
===================================================================
--- trunk/packages/gmod/gbrowse/trunk/debian/patches/debian-packaging-patch 2012-09-25 07:07:28 UTC (rev 12281)
+++ trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/debian-packaging-patch 2012-09-25 07:54:53 UTC (rev 12287)
@@ -1,230 +0,0 @@
-Patch to fit debian packaging - Olivier Sallou - February 2011
---- a/etc/init.d/gbrowse-slave
-+++ b/etc/init.d/gbrowse-slave
-@@ -1,10 +1,10 @@
- #!/bin/sh
- ### BEGIN INIT INFO
- # Provides: gbrowse_slave
--# Required-Start: $local_fs
--# Required-Stop: $local_fs
--# Default-Start: 28
--# Default-Stop: S
-+# 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.
- ### END INIT INFO
-
-@@ -13,7 +13,7 @@
- NAME="gbrowse-slave"
- DESC="GBrowse slave track rendering server"
-
--test -x $DAEMON || exit 0
-+#test -x $DAEMON || exit 0
- set -e
-
- USER=$WWWUSER
---- a/etc/default/gbrowse-slave
-+++ b/etc/default/gbrowse-slave
-@@ -1,10 +1,9 @@
--#!/bin/sh
-
- export PERL5LIB=$PERL5LIB
-
--DAEMON=$INSTALLSCRIPT/gbrowse_slave
--USER=$WWWUSER
--PRELOAD=$CONF/slave_preload.conf
-+DAEMON=/usr/bin/gbrowse_slave
-+USER=www-data
-+PRELOAD=/etc/gbrowse/slave_preload.conf
- RUNDIR=/var/run/gbrowse
- LOGDIR=/var/log/gbrowse
- PREFORK=3
---- a/bin/gbrowse_metadb_config.pl
-+++ b/bin/gbrowse_metadb_config.pl
-@@ -21,7 +21,10 @@
- my @argv = @ARGV;
-
- my ($dsn, $admin);
-+my $new=0;
-+
- GetOptions('dsn=s' => \$dsn,
-+ 'new' => \$new,
- 'admin=s' => \$admin) or die <<EOF;
- Usage: $0 [options] <optional path to GBrowse.conf>
-
-@@ -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 @@
- <dd><a href="example_scripts">/var/www/gbrowse2/example_scripts</a></dd>
- </dl>
-
--<h2>Example Databases</h2>
-+<h2>Example Databases (requires gbrowse-data package)</h2>
-
- <p>
-
-@@ -32,9 +32,9 @@
- installed for you. Try them at these URL:
-
- <ul>
--<li><a href="/cgi-bin/gb2/gbrowse/yeast">http://your.host/cgi-bin/gb2/gbrowse/yeast</a> (simple example)</li>
--<li><a href="/cgi-bin/gb2/gbrowse/yeast_advanced">http://your.host/cgi-bin/gb2/gbrowse/yeast_advanced</a> (advanced example)</li>
--<li><a href="/cgi-bin/gb2/gbrowse/yeast_renderfarm">http://your.host/cgi-bin/gb2/gbrowse/yeast_renderfarm</a> (yeast_renderfarm example)</li>
-+<li><a href="/cgi-bin/gbrowse/gbrowse/yeast">http://your.host/cgi-bin/gbrowse/gbrowse/yeast</a> (simple example)</li>
-+<li><a href="/cgi-bin/gbrowse/gbrowse/yeast_advanced">http://your.host/cgi-bin/gbrowse/gbrowse/yeast_advanced</a> (advanced example)</li>
-+<li><a href="/cgi-bin/gbrowse/gbrowse/yeast_renderfarm">http://your.host/cgi-bin/gbrowse/gbrowse/yeast_renderfarm</a> (yeast_renderfarm example)</li>
- </ul>
-
- <p>
-@@ -56,13 +56,13 @@
- <li><a href="/gb2/gbrowse/yeast">http://your.host/gb2/gbrowse/yeast</a></li>
- <li><a href="/gb2/gbrowse/yeast_advanced">http://your.host/gb2/gbrowse/yeast_advanced</a></li>
- <li><a href="/gb2/gbrowse/yeast_renderfarm">http://your.host/gb2/gbrowse/yeast_renderfarm</a></li>
--<li><a href="/gb2/gbrowse/pop_demo">http://your.host/gb2/gbrowse/pop_demo</a> (demo of embedded population allele frequency maps -- requires Template module to be installed)</li>
- </ul>
-
- <h3>Accelerated Demos</h3>
-
--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:
-
- <ul>
- <li>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 +423,83 @@
- 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 $perl, at inc,$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 || '';
-@@ -773,8 +851,9 @@
- 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
-@@ -161,9 +161,9 @@
- # "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.
Copied: trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/debian-packaging-patch (from rev 12283, trunk/packages/gmod/gbrowse/trunk/debian/patches/debian-packaging-patch)
===================================================================
--- trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/debian-packaging-patch (rev 0)
+++ trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/debian-packaging-patch 2012-09-25 07:54:53 UTC (rev 12287)
@@ -0,0 +1,235 @@
+Subject: fix directories for debian policy
+Description: Fix install directories to match
+ Debian Policy
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2012-09-25
+Forwarded: not-needed
+--- a/etc/init.d/gbrowse-slave
++++ b/etc/init.d/gbrowse-slave
+@@ -1,10 +1,10 @@
+ #!/bin/sh
+ ### BEGIN INIT INFO
+ # Provides: gbrowse_slave
+-# Required-Start: $local_fs
+-# Required-Stop: $local_fs
+-# Default-Start: 28
+-# Default-Stop: S
++# 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.
+ ### END INIT INFO
+
+@@ -13,7 +13,7 @@
+ NAME="gbrowse-slave"
+ DESC="GBrowse slave track rendering server"
+
+-test -x $DAEMON || exit 0
++#test -x $DAEMON || exit 0
+ set -e
+
+ USER=$WWWUSER
+--- a/etc/default/gbrowse-slave
++++ b/etc/default/gbrowse-slave
+@@ -1,10 +1,9 @@
+-#!/bin/sh
+
+ export PERL5LIB=$PERL5LIB
+
+-DAEMON=$INSTALLSCRIPT/gbrowse_slave
+-USER=$WWWUSER
+-PRELOAD=$CONF/slave_preload.conf
++DAEMON=/usr/bin/gbrowse_slave
++USER=www-data
++PRELOAD=/etc/gbrowse/slave_preload.conf
+ RUNDIR=/var/run/gbrowse
+ LOGDIR=/var/log/gbrowse
+ PREFORK=3
+--- a/bin/gbrowse_metadb_config.pl
++++ b/bin/gbrowse_metadb_config.pl
+@@ -21,7 +21,10 @@
+ my @argv = @ARGV;
+
+ my ($dsn, $admin);
++my $new=0;
++
+ GetOptions('dsn=s' => \$dsn,
++ 'new' => \$new,
+ 'admin=s' => \$admin) or die <<EOF;
+ Usage: $0 [options] <optional path to GBrowse.conf>
+
+@@ -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 @@
+ <dd><a href="example_scripts">/var/www/gbrowse2/example_scripts</a></dd>
+ </dl>
+
+-<h2>Example Databases</h2>
++<h2>Example Databases (requires gbrowse-data package)</h2>
+
+ <p>
+
+@@ -32,9 +32,9 @@
+ installed for you. Try them at these URL:
+
+ <ul>
+-<li><a href="/cgi-bin/gb2/gbrowse/yeast">http://your.host/cgi-bin/gb2/gbrowse/yeast</a> (simple example)</li>
+-<li><a href="/cgi-bin/gb2/gbrowse/yeast_advanced">http://your.host/cgi-bin/gb2/gbrowse/yeast_advanced</a> (advanced example)</li>
+-<li><a href="/cgi-bin/gb2/gbrowse/yeast_renderfarm">http://your.host/cgi-bin/gb2/gbrowse/yeast_renderfarm</a> (yeast_renderfarm example)</li>
++<li><a href="/cgi-bin/gbrowse/gbrowse/yeast">http://your.host/cgi-bin/gbrowse/gbrowse/yeast</a> (simple example)</li>
++<li><a href="/cgi-bin/gbrowse/gbrowse/yeast_advanced">http://your.host/cgi-bin/gbrowse/gbrowse/yeast_advanced</a> (advanced example)</li>
++<li><a href="/cgi-bin/gbrowse/gbrowse/yeast_renderfarm">http://your.host/cgi-bin/gbrowse/gbrowse/yeast_renderfarm</a> (yeast_renderfarm example)</li>
+ </ul>
+
+ <p>
+@@ -56,13 +56,13 @@
+ <li><a href="/gb2/gbrowse/yeast">http://your.host/gb2/gbrowse/yeast</a></li>
+ <li><a href="/gb2/gbrowse/yeast_advanced">http://your.host/gb2/gbrowse/yeast_advanced</a></li>
+ <li><a href="/gb2/gbrowse/yeast_renderfarm">http://your.host/gb2/gbrowse/yeast_renderfarm</a></li>
+-<li><a href="/gb2/gbrowse/pop_demo">http://your.host/gb2/gbrowse/pop_demo</a> (demo of embedded population allele frequency maps -- requires Template module to be installed)</li>
+ </ul>
+
+ <h3>Accelerated Demos</h3>
+
+-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:
+
+ <ul>
+ <li>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 $perl, at inc,$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 || '';
+@@ -773,8 +850,9 @@
+ 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
+@@ -161,9 +161,9 @@
+ # "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.
Deleted: trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/fix_pop_url
===================================================================
--- trunk/packages/gmod/gbrowse/trunk/debian/patches/fix_pop_url 2012-09-25 07:07:28 UTC (rev 12281)
+++ trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/fix_pop_url 2012-09-25 07:54:53 UTC (rev 12287)
@@ -1,25 +0,0 @@
-Author: Olivier Sallou <olivier.sallou at irisa.fr>
-Last-Update: 2011-08-08
-Description: update URL for details in example conf files to match /gb2 instead of cgi-bin/gb2
---- a/conf/yeast_chr1+2.conf
-+++ b/conf/yeast_chr1+2.conf
-@@ -158,7 +158,7 @@
- This gene brought to you by <a href="http://www.yeastgenome.org">SGD</a>.</th>
- <th bgcolor="cyan">Gene $name</th>
- </tr>
-- <tr align='left'><th><a href="/cgi-bin/gb2/gbrowse_details/yeast?name=$name" target="_new">See gene details</a></th></tr>
-+ <tr align='left'><th><a href="/gb2/gbrowse_details/yeast?name=$name" target="_new">See gene details</a></th></tr>
- <tr align='left'><th><a href="http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$name" target="_new">Ask SGD about $name</a></th></tr>
- <tr align='left'><th><a href="http://en.wikipedia.org/wiki/Special:Search?search=$name" target="_new">Ask Wikipedia about $name</a></th></tr>
- <tr align='left'><th><a href="http://www.google.com/search?q=$name" target="_new">Ask Google about $name</a></th></tr>
---- a/conf/yeast_renderfarm.conf
-+++ b/conf/yeast_renderfarm.conf
-@@ -153,7 +153,7 @@
- This gene brought to you by <a href="http://www.yeastgenome.org">SGD</a>.</th>
- <th bgcolor="cyan">Gene $name</th>
- </tr>
-- <tr align='left'><th><a href="/cgi-bin/gb2/gbrowse_details/yeast?name=$name" target="_new">See gene details</a></th></tr>
-+ <tr align='left'><th><a href="/gb2/gbrowse_details/yeast?name=$name" target="_new">See gene details</a></th></tr>
- <tr align='left'><th><a href="http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$name" target="_new">Ask SGD about $name</a></th></tr>
- <tr align='left'><th><a href="http://en.wikipedia.org/wiki/Special:Search?search=$name" target="_new">Ask Wikipedia about $name</a></th></tr>
- <tr align='left'><th><a href="http://www.google.com/search?q=$name" target="_new">Ask Google about $name</a></th></tr>
Copied: trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/fix_pop_url (from rev 12284, trunk/packages/gmod/gbrowse/trunk/debian/patches/fix_pop_url)
===================================================================
--- trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/fix_pop_url (rev 0)
+++ trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/fix_pop_url 2012-09-25 07:54:53 UTC (rev 12287)
@@ -0,0 +1,27 @@
+Subject: update URL for default conf
+Author: Olivier Sallou <olivier.sallou at irisa.fr>
+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 <a href="http://www.yeastgenome.org">SGD</a>.</th>
+ <th bgcolor="cyan">Gene $name</th>
+ </tr>
+- <tr align='left'><th><a href="/cgi-bin/gb2/gbrowse_details/yeast?name=$name" target="_new">See gene details</a></th></tr>
++ <tr align='left'><th><a href="/gb2/gbrowse_details/yeast?name=$name" target="_new">See gene details</a></th></tr>
+ <tr align='left'><th><a href="http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$name" target="_new">Ask SGD about $name</a></th></tr>
+ <tr align='left'><th><a href="http://en.wikipedia.org/wiki/Special:Search?search=$name" target="_new">Ask Wikipedia about $name</a></th></tr>
+ <tr align='left'><th><a href="http://www.google.com/search?q=$name" target="_new">Ask Google about $name</a></th></tr>
+--- a/conf/yeast_renderfarm.conf
++++ b/conf/yeast_renderfarm.conf
+@@ -153,7 +153,7 @@
+ This gene brought to you by <a href="http://www.yeastgenome.org">SGD</a>.</th>
+ <th bgcolor="cyan">Gene $name</th>
+ </tr>
+- <tr align='left'><th><a href="/cgi-bin/gb2/gbrowse_details/yeast?name=$name" target="_new">See gene details</a></th></tr>
++ <tr align='left'><th><a href="/gb2/gbrowse_details/yeast?name=$name" target="_new">See gene details</a></th></tr>
+ <tr align='left'><th><a href="http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$name" target="_new">Ask SGD about $name</a></th></tr>
+ <tr align='left'><th><a href="http://en.wikipedia.org/wiki/Special:Search?search=$name" target="_new">Ask Wikipedia about $name</a></th></tr>
+ <tr align='left'><th><a href="http://www.google.com/search?q=$name" target="_new">Ask Google about $name</a></th></tr>
Deleted: trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/gbrowse-slave-fix_defaults_path
===================================================================
--- trunk/packages/gmod/gbrowse/trunk/debian/patches/gbrowse-slave-fix_defaults_path 2012-09-25 07:07:28 UTC (rev 12281)
+++ trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/gbrowse-slave-fix_defaults_path 2012-09-25 07:54:53 UTC (rev 12287)
@@ -1,31 +0,0 @@
-Subject: fix default path on debian
-Author: Olivier Sallou <olivier.sallou at irisa.fr>
-Description: update path to be debian compliant, add description
-Last-Updated: 19/02/2012
---- 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
Copied: trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/gbrowse-slave-fix_defaults_path (from rev 12284, trunk/packages/gmod/gbrowse/trunk/debian/patches/gbrowse-slave-fix_defaults_path)
===================================================================
--- trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/gbrowse-slave-fix_defaults_path (rev 0)
+++ trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/gbrowse-slave-fix_defaults_path 2012-09-25 07:54:53 UTC (rev 12287)
@@ -0,0 +1,31 @@
+Subject: fix default path on debian
+Author: Olivier Sallou <olivier.sallou at irisa.fr>
+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
Deleted: trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/manpages.patch
===================================================================
--- trunk/packages/gmod/gbrowse/trunk/debian/patches/manpages.patch 2012-09-25 07:07:28 UTC (rev 12281)
+++ trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/manpages.patch 2012-09-25 07:54:53 UTC (rev 12287)
@@ -1,193 +0,0 @@
-Patch to correct POD-generated manual pages - Olivier Sallou - February 2011
---- 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)
-@@ -855,6 +861,8 @@
- croak "Do not call make_link() on the DataSource. Call it on the Render object";
- }
-
-+=over
-+
- =item $db = $dsn->databases
-
- Return all named databases from [name:database] tracks.
-@@ -1100,6 +1108,8 @@
- %DB_SETTINGS = ();
- }
-
-+=back
-+
- =head2 generate_image
-
- ($url,$path) = generate_image($gd);
Copied: trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/manpages.patch (from rev 12284, trunk/packages/gmod/gbrowse/trunk/debian/patches/manpages.patch)
===================================================================
--- trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/manpages.patch (rev 0)
+++ trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/manpages.patch 2012-09-25 07:54:53 UTC (rev 12287)
@@ -0,0 +1,216 @@
+Subject: fix POD-generated manual pages
+Description: upstream pages contain errors
+Author: Olivier Sallou <osallou at debian.org>
+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)
+@@ -855,6 +861,8 @@
+ croak "Do not call make_link() on the DataSource. Call it on the Render object";
+ }
+
++=over
++
+ =item $db = $dsn->databases
+
+ Return all named databases from [name:database] tracks.
+@@ -1100,6 +1108,8 @@
+ %DB_SETTINGS = ();
+ }
+
++=back
++
+ =head2 generate_image
+
+ ($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
+
Deleted: trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/skipRenderFarmTest_UpstreamBug12
===================================================================
--- trunk/packages/gmod/gbrowse/trunk/debian/patches/skipRenderFarmTest_UpstreamBug12 2012-09-25 07:07:28 UTC (rev 12281)
+++ trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/skipRenderFarmTest_UpstreamBug12 2012-09-25 07:54:53 UTC (rev 12287)
@@ -1,50 +0,0 @@
-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 <osallou at debian.org>
-Last-Updated: 07/03/2012
---- 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 $PID;
-
- BEGIN {
Copied: trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/skipRenderFarmTest_UpstreamBug12 (from rev 12284, trunk/packages/gmod/gbrowse/trunk/debian/patches/skipRenderFarmTest_UpstreamBug12)
===================================================================
--- trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/skipRenderFarmTest_UpstreamBug12 (rev 0)
+++ trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/skipRenderFarmTest_UpstreamBug12 2012-09-25 07:54:53 UTC (rev 12287)
@@ -0,0 +1,50 @@
+Subject: remove renderfarm tests
+Description: there is an upstream bug with renderfarm involved
+ tests. Upstream bug id 12 has been created witj instructions to
+ solve the issue. Runtime has been tested with no issue.
+ This patch remove tests using renderfarm feature.
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2012-03-07
+--- a/t/03.render.t
++++ b/t/03.render.t
+@@ -16,9 +16,10 @@
+ use lib "$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 {
Deleted: trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/skip_check_installed_test.patch
===================================================================
--- trunk/packages/gmod/gbrowse/trunk/debian/patches/skip_check_installed_test.patch 2012-09-25 07:07:28 UTC (rev 12281)
+++ trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/skip_check_installed_test.patch 2012-09-25 07:54:53 UTC (rev 12287)
@@ -1,35 +0,0 @@
-Author: Olivier Sallou <osallou at debian.org>
-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
-@@ -634,7 +634,7 @@
- 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);
- }
- }
-
-@@ -696,7 +696,7 @@
- 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;
- }
- }
- }
-@@ -734,7 +734,7 @@
- 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);
- }
- }
- }
Copied: trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/skip_check_installed_test.patch (from rev 12283, trunk/packages/gmod/gbrowse/trunk/debian/patches/skip_check_installed_test.patch)
===================================================================
--- trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/skip_check_installed_test.patch (rev 0)
+++ trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/skip_check_installed_test.patch 2012-09-25 07:54:53 UTC (rev 12287)
@@ -0,0 +1,35 @@
+Author: Olivier Sallou <osallou at debian.org>
+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
+@@ -633,7 +633,7 @@
+ 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);
+ }
+ }
+
+@@ -695,7 +695,7 @@
+ 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;
+ }
+ }
+ }
+@@ -733,7 +733,7 @@
+ 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);
+ }
+ }
+ }
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