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#!/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 <lincoln.stein@gmail.com>',
dist_abstract => 'The GMOD Generic Genome Browser',
license => 'perl',
requires => {
'perl' => '5.008',
'Bio::Root::Version' => '1.0069',
'Bio::Graphics' => '2.28',
'CGI::Session' => '4.02',
'Digest::MD5' => 0,
'ExtUtils::CBuilder' => 0,
'File::Temp' => 0,
'GD' => '2.07',
'Text::ParseWords' => '3.27',
'IO::String' => 0,
'JSON' => 0,
'LWP' => 0,
'Statistics::Descriptive' => 0,
'Storable' => 0,
'Time::HiRes' => 0,
'Digest::SHA' => 0,
'Date::Parse' => 0,
'Term::ReadKey' => 0,
},
build_requires => {'Capture::Tiny' => 0,},
recommends => {
'Bio::Das' => 0,
'Bio::DB::Sam' => 1.36,
'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,
'Net::OpenID::Consumer' => 0,
'Net::SMTP::SSL' => 0,
$] <= 5.008 ? ('Safe::World' => 0)
: () ,
'Template' => 2.20,
'Term::ReadKey' => 0,
},
script_files => [
'bin/gbrowse_clean.pl',
'bin/gbrowse_set_admin_passwd.pl',
'bin/gbrowse_import_ucsc_db.pl',
'bin/gbrowse_create_account.pl',
'bin/gbrowse_change_passwd.pl',
'bin/gbrowse_metadb_config.pl',
'bin/gbrowse_grow_cloud_vol.pl',
'bin/gbrowse_slave',
'bin/gbrowse_syn_load_alignment_database.pl',
'bin/gbrowse_syn_load_alignments_msa.pl',
'bin/make_das_conf.pl',
'bin/scan_gbrowse.pl',
'bin/wiggle2gff3.pl',
'bin/gtf2gff3.pl',
'bin/bed2gff3.pl',
'bin/ucsc_genes2gff.pl',
'bin/load_genbank.pl',
],
create_makefile_pl => 'passthrough',
);
print STDERR <<END;
**** WARNING *****************************************************************************************
If you are upgrading from an earlier version of GBrowse and wish to use named user accounts, please
set "user_accounts" to 1 in /etc/gbrowse2/GBrowse.conf and run bin/gbrowse_metadb_config.pl to
create/update your user account database.
See /etc/gbrowse2/GBrowse.conf.new for suggested settings.
******************************************************************************************************
END
#print STDERR "Continue? [y/n] ";
#my $line = <>;
#exit 0 unless $line =~ /[yY]/;
if(-e '/proc/filesystems'
&& `grep selinux /proc/filesystems`) {
print STDERR <<'END';
**** WARNING *********************************************************
You appear to have SELinux installed on this computer. This can
interfere with GBrowse operation. Please read the file
README.fedora_and_selinux in order to perform additional configuration
operations that may be necessary to run on this computer.
**********************************************************************
END
}
if ($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;
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