[med-svn] r6082 - in trunk/packages/gbrowse/trunk/debian: . patches source
olivier sallou
osallou-guest at alioth.debian.org
Thu Feb 24 08:45:32 UTC 2011
Author: osallou-guest
Date: 2011-02-24 08:45:26 +0000 (Thu, 24 Feb 2011)
New Revision: 6082
Added:
trunk/packages/gbrowse/trunk/debian/libgbrowse-perl.docs
trunk/packages/gbrowse/trunk/debian/libgbrowse-perl.manpages
trunk/packages/gbrowse/trunk/debian/patches/debian-packaging-patch
trunk/packages/gbrowse/trunk/debian/postinst
trunk/packages/gbrowse/trunk/debian/postrm
trunk/packages/gbrowse/trunk/debian/source/
trunk/packages/gbrowse/trunk/debian/source/format
Removed:
trunk/packages/gbrowse/trunk/debian/apache.conf
trunk/packages/gbrowse/trunk/debian/dirs
trunk/packages/gbrowse/trunk/debian/gbrowse.links
trunk/packages/gbrowse/trunk/debian/install
trunk/packages/gbrowse/trunk/debian/patches/blast2gff_1.69-and-usrbin.patch
Modified:
trunk/packages/gbrowse/trunk/debian/README.Debian
trunk/packages/gbrowse/trunk/debian/README.source
trunk/packages/gbrowse/trunk/debian/changelog
trunk/packages/gbrowse/trunk/debian/control
trunk/packages/gbrowse/trunk/debian/copyright
trunk/packages/gbrowse/trunk/debian/docs
trunk/packages/gbrowse/trunk/debian/patches/series
trunk/packages/gbrowse/trunk/debian/rules
trunk/packages/gbrowse/trunk/debian/watch
Log:
set gbrowse2
Modified: trunk/packages/gbrowse/trunk/debian/README.Debian
===================================================================
--- trunk/packages/gbrowse/trunk/debian/README.Debian 2011-02-24 07:58:30 UTC (rev 6081)
+++ trunk/packages/gbrowse/trunk/debian/README.Debian 2011-02-24 08:45:26 UTC (rev 6082)
@@ -1,11 +1,8 @@
GBrowse for Debian
----------------------------------
+------------------
-Current pacakging bugs :
-
- - Paths such as /home/charles/src/gbrowse-1.68/debian/gbrowse/var/www/gbrowse/databases in html files.
- - Owner of /var/www/gbrowse/database and gbrowse/tmp
- - MSG: Directory /tmp/test does not exist and you did not specify the -create flag
- - contrib scripts not installed.
-
- -- Charles Plessy <charles-debian-nospam at plessy.org> Wed, 13 Jun 2007 19:07:01 +0900
+ GBrowse needs a web browser to run. If Apache2 is installed, a default configuration file
+ has been installed in /etc/apache2/conf.d to map URLs to GBrowse directories.
+ In other cases (other web server, apache not installed...), one should configure the web
+ server to trigger gbrowse. An apache2 template is available in configration directory
+ (/etc/gbrowse2/apache2.conf).
Modified: trunk/packages/gbrowse/trunk/debian/README.source
===================================================================
--- trunk/packages/gbrowse/trunk/debian/README.source 2011-02-24 07:58:30 UTC (rev 6081)
+++ trunk/packages/gbrowse/trunk/debian/README.source 2011-02-24 08:45:26 UTC (rev 6082)
@@ -1,9 +1,4 @@
-gbrowse source package
-━━━━━━━━━━━━━━━━━━━━━━
+GBrowse for Debian
+-----------------
-This package uses the ‘quilt’ program to patch the original upstream sources.
-This is documented in ‘/usr/share/doc/quilt/README.source’.
-
-This package is maintained by the Debian Med packaging team in a Subversion
-repository (see debian/control). All Debian Developers have commit rights on
-it.
+ Source file can be watched vi a watch file. However, to build the package for debian, one needs to update an installation script to install_util/GBrowseInstall.pm. Code has been patched to do so. At build time, thereis a request to register, one should select no as it is non sense at build time.
Deleted: trunk/packages/gbrowse/trunk/debian/apache.conf
===================================================================
--- trunk/packages/gbrowse/trunk/debian/apache.conf 2011-02-24 07:58:30 UTC (rev 6081)
+++ trunk/packages/gbrowse/trunk/debian/apache.conf 2011-02-24 08:45:26 UTC (rev 6082)
@@ -1,13 +0,0 @@
-# I used /etc/gallery2/apache.conf as a template. -- Charles Plessy
-Alias /gbrowse /usr/share/gbrowse
-
-<Directory /usr/share/gbrowse>
- Options FollowSymLinks
-# AllowOverride Limit Options FileInfo
-</Directory>
-
-# some people prefer a simple URL like http://gbrowse.example
-#<VirtualHost *:80>
-# DocumentRoot /usr/share/gbrowse
-# ServerName gbrowse.example
-#</VirtualHost>
Modified: trunk/packages/gbrowse/trunk/debian/changelog
===================================================================
--- trunk/packages/gbrowse/trunk/debian/changelog 2011-02-24 07:58:30 UTC (rev 6081)
+++ trunk/packages/gbrowse/trunk/debian/changelog 2011-02-24 08:45:26 UTC (rev 6082)
@@ -1,5 +1,5 @@
-gbrowse (1.70-1) UNRELEASED; urgency=low
+libgbrowse-perl (2.26-1) unstable; urgency=low
- * Initial release (Closes: #429610)
+ * Initial Release (Closes: #429610).
- -- Charles Plessy <plessy at debian.org> Tue, 26 Aug 2008 18:52:23 +0900
+ -- Olivier Sallou <olivier.sallou at irisa.fr> Sat, 29 Jan 2011 21:55:43 +0100
Modified: trunk/packages/gbrowse/trunk/debian/control
===================================================================
--- trunk/packages/gbrowse/trunk/debian/control 2011-02-24 07:58:30 UTC (rev 6081)
+++ trunk/packages/gbrowse/trunk/debian/control 2011-02-24 08:45:26 UTC (rev 6082)
@@ -1,31 +1,33 @@
-Source: gbrowse
+Source: libgbrowse-perl
Section: science
Priority: optional
+Build-Depends: bioperl (>= 1.5.9), debhelper (>= 7.0.17),perl-depends,
+ libbio-graphics-perl (>= 2.09), libcapture-tiny-perl,
+ 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, perl,
+ perl (>= 5.10.0) | libextutils-cbuilder-perl, sqlite3,libdbd-sqlite3-perl, quilt, libterm-readkey-perl
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Olivier Sallou <olivier.sallou at irisa.fr>
DM-Upload-Allowed: yes
-Uploaders: Charles Plessy <plessy at debian.org>
-Build-Depends: debhelper (>= 7), quilt,
- libio-string-perl, libbio-graphics-perl (>= 1.97), bioperl (>= 1.6),
- libcgi-session-perl (>= 4.02), libgd-gd2-perl (>= 2.07),
- libstatistics-descriptive-perl, libbio-db-das-chado-perl, perl
-Standards-Version: 3.7.3
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/gbrowse/trunk/?rev=0&sc=0
-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/gbrowse/trunk/
-Homepage: http://gmod.org/wiki/GBrowse
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/biomaj/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/biomaj/trunk/?rev=0&sc=0
+Standards-Version: 3.9.1
+Homepage: http://search.cpan.org/dist/GBrowse/
-Package: gbrowse
-Architecture: any
-Depends: ${perl:Depends}, ${shlibs:Depends}, ${misc:Depends},
- libio-string-perl, libbio-graphics-perl (>= 1.97), bioperl (>= 1.6),
- libcgi-session-perl (>= 4.02), libgd-gd2-perl (>= 2.07),
- libstatistics-descriptive-perl
-# The above line comes from dh-make-perl
-Recommends: libdbd-mysql-perl, libdb4.4
-# Should probably also recomment mod-perl
-Description: The generic genome browser component of the GMOD project
- The 'generic genome browser' component of the Generic Model Organism Database
- toolkit (GMOD) is a combination of database and interactive Web page for
- manipulating and displaying annotations on genomes. Some of its features:
+Package: libgbrowse-perl
+Architecture: any
+Depends: ${misc:Depends}, ${perl:Depends}, ${shlibs:Depends},
+ bioperl (>= 1.5.9), libbio-graphics-perl (>= 2.09),
+ 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, perl,
+ perl (>= 5.10.0) | libextutils-cbuilder-perl, libterm-readkey-perl, sqlite3, libdbd-sqlite3-perl, libterm-readkey-perl
+Description: The GMOD Generic Genome Browser
+ The 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;
Modified: trunk/packages/gbrowse/trunk/debian/copyright
===================================================================
--- trunk/packages/gbrowse/trunk/debian/copyright 2011-02-24 07:58:30 UTC (rev 6081)
+++ trunk/packages/gbrowse/trunk/debian/copyright 2011-02-24 08:45:26 UTC (rev 6082)
@@ -1,29 +1,28 @@
-This package was debianized by Charles Plessy <charles-debian-nospam at plessy.org> on
-Wed, 13 Jun 2007 19:07:01 +0900.
+Format-Specification: http://svn.debian.org/wsvn/dep/web/deps/dep5.mdwn?op=file&rev=135
+Maintainer: Lincoln Stein <lincoln.stein at gmail.com>
+Source: http://search.cpan.org/dist/GBrowse/
+Name: GBrowse
-It was downloaded from <fill in http/ftp site>
+Files: *
+Copyright: Lincoln Stein <lincoln.stein at gmail.com>
+License: Artistic or GPL-1+
-Upstream Author: <put author(s) name and email here>
+Files: debian/*
+Copyright: 2011, Olivier Sallou <olivier.sallou at irisa.fr>
+License: Artistic or GPL-1+
-Copyright: <put the year(s) of the copyright, and the names of the
- copyright holder(s) here>
+License: Artistic
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the Artistic License, which comes with Perl.
+ .
+ On Debian GNU/Linux systems, the complete text of the Artistic License
+ can be found in `/usr/share/common-licenses/Artistic'.
-License:
-
- This program is free software; you can redistribute it and/or modify it
- under the terms of the "Artistic License" which comes with Debian.
-
- THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
- WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES
- OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-
-On Debian systems, the complete text of the Artistic License
-can be found in `/usr/share/common-licenses/Artistic'.
-
-The Debian packaging is (C) 2007, Charles Plessy <charles-debian-nospam at plessy.org> and
-is licensed under the GPL, see `/usr/share/common-licenses/GPL'.
-
-
-# Please also look if there are files or directories which have a
-# different copyright/license attached and list them here.
-
+License: GPL-1+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 1, or (at your option)
+ any later version.
+ .
+ On Debian GNU/Linux systems, the complete text of version 1 of the
+ General Public License can be found in `/usr/share/common-licenses/GPL-1'.
Deleted: trunk/packages/gbrowse/trunk/debian/dirs
===================================================================
--- trunk/packages/gbrowse/trunk/debian/dirs 2011-02-24 07:58:30 UTC (rev 6081)
+++ trunk/packages/gbrowse/trunk/debian/dirs 2011-02-24 08:45:26 UTC (rev 6082)
@@ -1,2 +0,0 @@
-usr/bin
-usr/share/man/man1
Modified: trunk/packages/gbrowse/trunk/debian/docs
===================================================================
--- trunk/packages/gbrowse/trunk/debian/docs 2011-02-24 07:58:30 UTC (rev 6081)
+++ trunk/packages/gbrowse/trunk/debian/docs 2011-02-24 08:45:26 UTC (rev 6082)
@@ -1,4 +1,3 @@
README
README.gff3
-README.sessions
-TODO
+INSTALL
Deleted: trunk/packages/gbrowse/trunk/debian/gbrowse.links
===================================================================
--- trunk/packages/gbrowse/trunk/debian/gbrowse.links 2011-02-24 07:58:30 UTC (rev 6081)
+++ trunk/packages/gbrowse/trunk/debian/gbrowse.links 2011-02-24 08:45:26 UTC (rev 6082)
@@ -1 +0,0 @@
-etc/gbrowse.conf/apache.conf etc/apache2/conf.d/gbrowse
Deleted: trunk/packages/gbrowse/trunk/debian/install
===================================================================
--- trunk/packages/gbrowse/trunk/debian/install 2011-02-24 07:58:30 UTC (rev 6081)
+++ trunk/packages/gbrowse/trunk/debian/install 2011-02-24 08:45:26 UTC (rev 6082)
@@ -1 +0,0 @@
-debian/apache.conf etc/gbrowse.conf
Added: trunk/packages/gbrowse/trunk/debian/libgbrowse-perl.docs
===================================================================
--- trunk/packages/gbrowse/trunk/debian/libgbrowse-perl.docs (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/libgbrowse-perl.docs 2011-02-24 08:45:26 UTC (rev 6082)
@@ -0,0 +1,17 @@
+README
+README.GBrowse-2.00
+README.gff3
+README.IF.GBROWSE.ISNT.WORKING
+README.fedora_and_selinux
+docs/README.tutorial
+docs/developer_notes/README.sharing_tracks
+docs/developer_notes/README.rearchitecture
+sample_data/admin_uploads/README
+libalign/README
+t/testdata/phylo_align/readme.txt
+contrib/README
+contrib/install_macosx/README.html
+contrib/GeneFinder/genefinder/README
+contrib/SynView/README
+contrib/TextDumper/README
+contrib/Coverage/README
Added: trunk/packages/gbrowse/trunk/debian/libgbrowse-perl.manpages
===================================================================
--- trunk/packages/gbrowse/trunk/debian/libgbrowse-perl.manpages (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/libgbrowse-perl.manpages 2011-02-24 08:45:26 UTC (rev 6082)
@@ -0,0 +1 @@
+docs/gbrowse.1
Deleted: trunk/packages/gbrowse/trunk/debian/patches/blast2gff_1.69-and-usrbin.patch
===================================================================
--- trunk/packages/gbrowse/trunk/debian/patches/blast2gff_1.69-and-usrbin.patch 2011-02-24 07:58:30 UTC (rev 6081)
+++ trunk/packages/gbrowse/trunk/debian/patches/blast2gff_1.69-and-usrbin.patch 2011-02-24 08:45:26 UTC (rev 6082)
@@ -1,19 +0,0 @@
-Index: gbrowse-1.68/contrib/blast2gff.pl
-===================================================================
---- gbrowse-1.68.orig/contrib/blast2gff.pl 2007-06-26 11:59:12.000000000 +0900
-+++ gbrowse-1.68/contrib/blast2gff.pl 2007-06-26 11:59:55.000000000 +0900
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl -w
-+#!/usr/bin/perl -w
-
- =head1 NAME
-
-@@ -271,7 +271,7 @@
- replace_undef($hsp->query->end);
- }
- else {
-- $hsp_col9_class_name = upper_case_first_letter(replace_undef($default_hsp_col3_feature_type))." ".
-+ $hsp_col9_class_name = upper_case_first_letter(replace_undef($default_match_col3_feature_type))." ".
- replace_undef($result->query_name);
- }
-
Added: trunk/packages/gbrowse/trunk/debian/patches/debian-packaging-patch
===================================================================
--- trunk/packages/gbrowse/trunk/debian/patches/debian-packaging-patch (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/patches/debian-packaging-patch 2011-02-24 08:45:26 UTC (rev 6082)
@@ -0,0 +1,144 @@
+Patch to fit debian packaging - Olivier Sallou - February 2011
+--- /dev/null
++++ b/docs/gbrowse.1
+@@ -0,0 +1,45 @@
++.TH GBrowse2 1 "February 07, 2011" "version 1.1.0" "USER COMMANDS"
++.SH NAME
++GBrowse2 \- The Generic Genome Browser
++.SH SYNOPSIS
++.B libgbrowse-perl
++[\-h]
++.SH INSTALLATION
++If Apache2 is installed on the system, the software has configured it to link URLs to GBrowse directories. A restart of Apache is required to take it into account. Configuration is available in /etc/gbrowse2/apache2.conf file.
++ If an other web server is used, one should refer to the apache2 template to map urls in the same way.
++.PP
++.SH DEPENDENCIES
++Additional optional perl dependencies exist to provide additional features. Please refer to Optional modules in INSTALL file for more information.
++.PP
++.SH CONFIGURATION
++.B gbrowse2
++Configuration files are located in /etc/gbrowse2. Main configuration file is GBrowse.conf. It contains the global configuration elements. Specific configuration files are located in the same directory per data bank. For more details, one should refer to the GBrowse documentation.
++ Installation is provided with a Yeast genome sample.
++.PP
++.SH DESCRIPTION
++GBrowse 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).
++.PP
++.SH WEB ACCESS
++GBrowse is accessible at URL http://localhost/gbrowse2
++.PP
++.SH AUTHOR
++Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging
++Lincoln Stein - GBrowse
+--- a/install_util/GBrowseInstall.pm
++++ b/install_util/GBrowseInstall.pm
+@@ -403,6 +403,84 @@
+ 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;
++
++}
++
++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 || '';
+@@ -489,6 +567,7 @@
+ $self->SUPER::ACTION_install();
+ }
+
++
+ sub ACTION_debian {
+ my $self = shift;
+ system "debuild";
Modified: trunk/packages/gbrowse/trunk/debian/patches/series
===================================================================
--- trunk/packages/gbrowse/trunk/debian/patches/series 2011-02-24 07:58:30 UTC (rev 6081)
+++ trunk/packages/gbrowse/trunk/debian/patches/series 2011-02-24 08:45:26 UTC (rev 6082)
@@ -1 +1 @@
-#blast2gff_1.69-and-usrbin.patch
+debian-packaging-patch
Added: trunk/packages/gbrowse/trunk/debian/postinst
===================================================================
--- trunk/packages/gbrowse/trunk/debian/postinst (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/postinst 2011-02-24 08:45:26 UTC (rev 6082)
@@ -0,0 +1,38 @@
+#!/bin/bash
+
+set -e
+
+# Source debconf library.
+. /usr/share/debconf/confmodule
+
+#DEBHELPER#
+
+if [ -e /var/cache/gbrowse2 ]
+then
+ echo "Dir already present, skip it"
+else
+mkdir -p /var/cache/gbrowse2
+fi
+
+chown -R root:www-data /usr/share/gbrowse2/databases
+chmod -R 770 /usr/share/gbrowse2/databases
+chown -R root:www-data /var/cache/gbrowse2
+chmod -R 770 /var/cache/gbrowse2
+# Initialize account database
+perl /bin/gbrowse_metadb_config.pl
+chown -R www-data:www-data /var/cache/gbrowse2/sessions
+
+
+if [ -e /etc/apache2/conf.d ]
+then
+ if [ -e /etc/apache2/conf.d/gbrowse2 ]
+ then
+ echo "Apache config already set, keeping original"
+ else
+ ln -s /etc/gbrowse2/apache2.conf /etc/apache2/conf.d/gbrowse2
+ echo "Warning, apache2 must be restarted to take into account the configuration"
+ fi
+fi
+
+update-rc.d gbrowse-slave defaults
+
Added: trunk/packages/gbrowse/trunk/debian/postrm
===================================================================
--- trunk/packages/gbrowse/trunk/debian/postrm (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/postrm 2011-02-24 08:45:26 UTC (rev 6082)
@@ -0,0 +1,32 @@
+#!/bin/bash
+
+set -e
+
+# Source debconf library.
+. /usr/share/debconf/confmodule
+
+#DEBHELPER#
+
+rm -rf /var/cache/gbrowse2
+
+if [ -e /etc/apache2/conf.d/gbrowse2 ]
+then
+ rm /etc/apache2/conf.d/gbrowse2
+fi
+
+if [ -e /usr/share/gbrowse2 ]
+then
+rm -rf /usr/share/gbrowse2
+fi
+
+if [ "$1" = "purge" ]; then
+update-rc.d gbrowse-slave remove
+ if [ -e /etc/init.d/gbrowse-slave ]
+ then
+ rm /etc/init.d/gbrowse-slave
+ fi
+ if [ -e /etc/default/gbrowse-slave ]
+ then
+ rm /etc/default/gbrowse-slave
+ fi
+fi
Modified: trunk/packages/gbrowse/trunk/debian/rules
===================================================================
--- trunk/packages/gbrowse/trunk/debian/rules 2011-02-24 07:58:30 UTC (rev 6081)
+++ trunk/packages/gbrowse/trunk/debian/rules 2011-02-24 08:45:26 UTC (rev 6082)
@@ -1,71 +1,77 @@
#!/usr/bin/make -f
-# This debian/rules file is provided as a template for normal perl
-# packages. It was created by Marc Brockschmidt <marc at dch-faq.de> for
-# the Debian Perl Group (http://pkg-perl.alioth.debian.org/) but may
-# be used freely wherever it is useful.
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
+#%:
+# dh $@
-include /usr/share/quilt/quilt.make
-# If set to a true value then MakeMaker's prompt function will
-# always return the default without waiting for user input.
-export PERL_MM_USE_DEFAULT=1
-
-PERL ?= /usr/bin/perl
-PACKAGE = $(shell dh_listpackages)
-TMP = $(CURDIR)/debian/$(PACKAGE)
-
-# Allow disabling build optimisation by setting noopt in
-# $DEB_BUILD_OPTIONS
-CFLAGS = -Wall -g
-ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
- CFLAGS += -O0
-else
- CFLAGS += -O2
-endif
-
-build: patch build-stamp
+build: configure build-stamp
build-stamp:
dh_testdir
- # Add commands to compile the package here
- $(PERL) Makefile.PL \
- INSTALLDIRS=vendor \
- PACKAGE_DIR=$(TMP) \
- PREFIX=$(TMP) \
- APACHE=$(TMP)/etc/apache2 \
- CONF=$(TMP)/etc \
- CGIBIN=$(TMP)/usr/lib/cgi-bin \
- HTDOCS=$(TMP)/usr/share \
- GBROWSE_ROOT=gbrowse \
- DO_XS=1
- $(MAKE) OPTIMIZE="$(CFLAGS)" LD_RUN_PATH=""
- $(MAKE) test
+ #perl Build.PL --install_path lib=/usr/lib/perl5 --conf=/etc/gbrowse2 --htdocs=/usr/share/gbrowse2/htdocs --tmp=/var/cache/gbrowse2 --databases=/usr/share/gbrowse2/databases --cgibin=/usr/lib/cgi-bin/gbrowse2 --www-user=www-data --installetc=y
+ dh_auto_build
+ dh_auto_test
touch $@
-clean: unpatch
- dh clean
+clean:
+ dh $@
+
install: install-stamp
install-stamp: build-stamp
- dh_testdir
dh_testroot
dh_prep
- # Add commands to install the package into $(TMP)
- $(MAKE) install DESTDIR=$(TMP) PREFIX=/usr
- [ ! -d $(TMP)/usr/share/perl5 ] || \
- rmdir --ignore-fail-on-non-empty --parents --verbose \
- $(TMP)/usr/share/perl5
+ dh_installdirs
+ #dh_auto_install
+ perl Build.PL --conf=/etc/gbrowse2 --htdocs=/usr/share/gbrowse2/htdocs --tmp=/var/cache/gbrowse2 --databases=/usr/share/gbrowse2/databases --cgibin=/usr/lib/cgi-bin/gbrowse2 --www-user=www-data
+ ./Build --install_base=debian/libgbrowse-perl debianinstall
+ ./Build apache_conf > debian/libgbrowse-perl/etc/gbrowse2/apache2.conf
+ perl Build.PL --conf=/etc/gbrowse2 --htdocs=/usr/share/gbrowse2/htdocs --tmp=/var/cache/gbrowse2 --databases=/usr/share/gbrowse2/databases --cgibin=/usr/lib/cgi-bin/gbrowse2 --www-user=www-data --installetc=y
+ ./Build --install_base=debian/libgbrowse-perl install_slave
+ mkdir -p debian/libgbrowse-perl/usr/lib/perl5
+ mv debian/libgbrowse-perl/lib/perl5/*/* debian/libgbrowse-perl/usr/lib/perl5/
+ rm -rf debian/libgbrowse-perl/lib
+ dh_install
+ dh_installdocs
+ dh_installchangelogs
+ dh_installexamples
+ dh_installman
+ dh_installcatalogs
+ dh_installcron
+ dh_installdebconf
+ dh_installemacsen
+ dh_installifupdown
+ dh_installinfo
+ dh_pysupport
+ dh_installinit
+ dh_installmenu
+ dh_installmime
+ dh_installmodules
+ dh_installlogcheck
+ dh_installlogrotate
+ dh_installpam
+ dh_installppp
+ dh_installudev
+ dh_installwm
+ dh_installxfonts
+ dh_bugfiles
+ dh_lintian
+ dh_gconf
+ dh_icons
+ dh_perl
+ dh_usrlocal
+ dh_link
+ dh_compress
+ dh_fixperms
touch $@
-# Build architecture-independent files here.
-binary-indep: build install
-# We have nothing to do here for an architecture-dependent package
+binary-arch: install
+ dh $@
-# Build architecture-dependent files here.
-binary-arch: build install
- dh binary-arch
+binary-indep:
-binary: binary-indep binary-arch
-.PHONY: build clean binary-indep binary-arch binary install
+binary: binary-arch binary-indep
+
+.PHONY: binary binary-arch binary-indep install clean build configure
+
+
+
Added: trunk/packages/gbrowse/trunk/debian/source/format
===================================================================
--- trunk/packages/gbrowse/trunk/debian/source/format (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/source/format 2011-02-24 08:45:26 UTC (rev 6082)
@@ -0,0 +1 @@
+3.0 (quilt)
Modified: trunk/packages/gbrowse/trunk/debian/watch
===================================================================
--- trunk/packages/gbrowse/trunk/debian/watch 2011-02-24 07:58:30 UTC (rev 6081)
+++ trunk/packages/gbrowse/trunk/debian/watch 2011-02-24 08:45:26 UTC (rev 6082)
@@ -1,2 +1,2 @@
version=3
-http://sf.net/gmod/Generic-Genome-Browser-(.*)\.tar\.gz
+http://search.cpan.org/dist/GBrowse/ .*/GBrowse-v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$
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