this was the previous trunk branch

Author: lstein

.cvsignore

@@ -0,0 +1,25 @@
+GGB.def
+_build*
+benchmarking
+blib*
+*.patch
+*gz
+*.notes
+pm_to_blib
+*.tmp
+test*
+tmp*
+Build
+Makefile
+okada*
+META.yml
+old_tar_files
+*.tar
+INSTALL.SKIP
+NFS_bechmark_results.ods
+*-stamp
+foo*
+.cvsignore
+*.index
+
+

Build.PL

@@ -0,0 +1,128 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+use FindBin '$Bin';
+
+use lib "$Bin/install_util";
+use File::Copy;
+use GBrowseInstall;
+
+my $build = GBrowseInstall->new(
+    module_name        => 'GBrowse',
+    dist_version_from  => 'lib/Bio/Graphics/Browser2.pm',
+    dist_author        => 'Lincoln Stein <[email protected]>',
+    dist_abstract      => 'The GMOD Generic Genome Browser',
+    license            => 'perl',
+
+    requires     => {
+	'perl'                => '5.008',
+	'Bio::Root::Version'  => '1.005009001',
+	'Bio::Graphics'       => '2.09',
+	'CGI::Session'        => '4.02',
+	'Digest::MD5'         => 0,	
+        'ExtUtils::CBuilder'  => 0,
+	'File::Temp'          => 0,
+	'GD'                  => '2.07',
+	'IO::String'          => 0,
+	'JSON'                => 0,
+	'LWP'                 => 0,
+	'Statistics::Descriptive'  => 0,
+	'Storable'            => 0,
+    },
+    build_requires => {'Capture::Tiny'       => 0,},
+    recommends  => {
+        'Ace'                      => 0,
+	'Bio::Das'                 => 0,
+	'Bio::DB::Sam'             => 1.20,
+	'Bio::DB::BigFile'         => 1.00,
+	'Crypt::SSLeay'            => 0,
+	'DB_File::Lock'            => 0,
+	'DBI'                      => 0,
+	'DBD::mysql'               => 0,
+	'DBD::Pg'                  => 0,
+	'DBD::SQLite'              => 0,
+	'Digest::SHA'              => 0,	
+	'FCGI'                     => 0,
+	'File::NFSLock'            => 0,
+	'GD::SVG'                  => 0,
+	'Math::BigInt'             => 0,
+#	'MOBY::Client::Central'    => 0,
+	'Net::OpenID::Consumer'    => 0,
+	'Net::SMTP::SSL'           => 0,
+	$] <= 5.008 ? ('Safe::World'  => 0)
+                    : ()               ,
+	'Template'                 => 2.20,
+    },
+    script_files => [
+	'bin/gbrowse_clean.pl',
+	'bin/gbrowse_create_useraccount_db.pl',
+	'bin/gbrowse_set_admin_passwd.pl',
+	'bin/gbrowse_slave',
+        'bin/gbrowse_syn_load_alignment_database.pl',
+        'bin/gbrowse_syn_load_alignments_msa.pl',
+	'bin/make_das_conf.pl',
+	'bin/wiggle2gff3.pl',
+# not sure if these still work
+#	'bin/register_moby_services.pl',
+#	'bin/process_wormbase.pl',
+#	'bin/process_sgd.pl',
+#	'bin/load_genbank.pl',
+    ],
+
+    create_makefile_pl => 'passthrough',
+
+    );
+
+if(-e '/proc/filesystems' 
+   && `grep selinux /proc/filesystems`) {
+    print STDERR <<'END';
+**** WARNING *********************************************************
+You appear to have SELinux installed on this computer. This can
+interfere with GBrowse operation. Please read the file
+README.fedora_and_selinux in order to perform additional configuration
+operations that may be necessary to run on this computer.
+**********************************************************************
+END
+}
+
+if ($build->have_c_compiler()) {
+    foreach ('CAlign.xs','CAlign.pm') {
+	copy("./libalign/$_" => "./lib/Bio/Graphics/Browser/$_");
+    }
+    $build->include_dirs(["$Bin/libalign"]);
+}
+
+my $argc=0;
+for my $arg (keys %{$build->private_props}) {
+    my $value = $build->runtime_params($arg) or next;
+    $build->config_data($arg=>$value);
+    $argc++;
+}
+$build->config_data(OpenIDConsumerSecret=>int(1e15*rand()));
+$build->config_done(1) if $argc > 0;
+
+$build->add_build_element('conf');
+$build->add_build_element('htdocs');
+$build->add_build_element('cgibin');
+$build->add_build_element('etc');
+$build->add_build_element('database');
+
+$build->create_build_script;
+print STDERR <<END;
+Now run:
+  ./Build test
+  ./Build demo          (optional)
+  ./Build install       (as superuser/administrator)
+        -or-
+  ./Build install_slave (optional, for slave installations)
+
+Other useful targets:
+  ./Build register      (to register your copy of GBrowse)
+  ./Build reconfig      (to reconfigure install locations)
+  ./Build demostop      (to stop the demo)
+END
+
+exit 0;
+
+1;

Changes

@@ -0,0 +1,26 @@
+The Generic Genome Browser package versions between 1.0 and 1.8 and
+all associated files are Copyright (c) 2002 Cold Spring Harbor
+Laboratory and University of California, Berkeley. Versions 1.9 and
+higher are copyright (c) 2010 Ontario Institute for Cancer Research.
+
+This package and its accompanying libraries is free software; you can
+redistribute it and/or modify it under the terms of the GPL (either
+version 1, or at your option, any later version) or the Artistic
+License 2.0.  Refer to LICENSE for the full license text.
+
+CSHL makes no representations whatsoever as to the SOFTWARE contained
+herein.  It is experimental in nature and is provided WITHOUT WARRANTY
+OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER
+WARRANTY, EXPRESS OR IMPLIED.  CSHL MAKES NO REPRESENTATION OR
+WARRANTY THAT THE USE OF THIS SOFTWARE WILL NOT INFRINGE ANY PATENT OR
+OTHER PROPRIETARY RIGHT.
+
+By downloading this SOFTWARE, your Institution hereby indemnifies CSHL
+against any loss, claim, damage or liability, of whatsoever kind or
+nature, which may arise from your Institution's respective use,
+handling or storage of the SOFTWARE.
+
+If publications result from research using this SOFTWARE, we ask that
+CSHL, University of California, Berkeley and the Ontario Institute for
+Cancer Research be acknowledged and/or credit be given to
+CSHL/Berkeley/OICR scientists, as scientifically appropriate.