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 <[email protected]> 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 <[email protected]> Sun, 19 Feb 2012 15:59:53 +0100 - -gbrowse (2.42~dfsg-1) unstable; urgency=low - - * New upstream release - - -- Olivier Sallou <[email protected]> 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 <[email protected]> Mon, 29 Aug 2011 10:34:12 -0400 - - -gbrowse (2.39~dfsg-1) unstable; urgency=low - - * New upstream version - - -- Olivier Sallou <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Tue, 26 Apr 2011 21:46:23 -0400 - -gbrowse (2.26~dfsg-1) experimental; urgency=low - - [ Olivier Sallou ] - * Initial Release (Closes: #429610). - - -- Charles Plessy <[email protected]> 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 <[email protected]> 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 <[email protected]> Sun, 19 Feb 2012 15:59:53 +0100 + +gbrowse (2.42~dfsg-1) unstable; urgency=low + + * New upstream release + + -- Olivier Sallou <[email protected]> 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 <[email protected]> Mon, 29 Aug 2011 10:34:12 -0400 + + +gbrowse (2.39~dfsg-1) unstable; urgency=low + + * New upstream version + + -- Olivier Sallou <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Tue, 26 Apr 2011 21:46:23 -0400 + +gbrowse (2.26~dfsg-1) experimental; urgency=low + + [ Olivier Sallou ] + * Initial Release (Closes: #429610). + + -- Charles Plessy <[email protected]> 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 <[email protected]> -Uploaders: Olivier Sallou <[email protected]>, - Charles Plessy <[email protected]>, Aaron M. Ucko <[email protected]> -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 <[email protected]> +Uploaders: Olivier Sallou <[email protected]>, + Charles Plessy <[email protected]>, Aaron M. Ucko <[email protected]> +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 $perl,@inc,$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 <[email protected]> +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 $perl,@inc,$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 <[email protected]> -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 <[email protected]> +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 <[email protected]> -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 <[email protected]> +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 <[email protected]> +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 <[email protected]> -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 $PID; - - BEGIN { Copied: trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/skipRenderFarmTest_UpstreamBug12 (from rev 12284, trunk/packages/gmod/gbrowse/trunk/debian/patches/skipRenderFarmTest_UpstreamBug12) =================================================================== --- trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/skipRenderFarmTest_UpstreamBug12 (rev 0) +++ trunk/packages/gmod/gbrowse/tags/2.51+dfsg-1/debian/patches/skipRenderFarmTest_UpstreamBug12 2012-09-25 07:54:53 UTC (rev 12287) @@ -0,0 +1,50 @@ +Subject: remove renderfarm tests +Description: there is an upstream bug with renderfarm involved + tests. Upstream bug id 12 has been created witj instructions to + solve the issue. Runtime has been tested with no issue. + This patch remove tests using renderfarm feature. +Author: Olivier Sallou <[email protected]> +Last-Updated: 2012-03-07 +--- a/t/03.render.t ++++ b/t/03.render.t +@@ -16,9 +16,10 @@ + use lib "$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 <[email protected]> -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 <[email protected]> +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); + } + } + } _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
