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merged in Lincoln's additions and swapped mirrors 1 and 2 for sourcef…
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…orge since 1 is failing right now (if that continues, we should look at putting a different server in).
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Scott Cain committed Dec 5, 2008
1 parent 389bda5 commit 212bece
Showing 1 changed file with 33 additions and 19 deletions.
52 changes: 33 additions & 19 deletions bin/gbrowse_netinstall.pl
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@@ -1,4 +1,3 @@
#
#/usr/bin/perl

=head1 NAME
Expand All @@ -14,7 +13,7 @@ =head1 SYNOPSIS
-h|--help Show this message
-d|--dev Use the developement version of both GBrowse
and bioperl from CVS
--bioperl_dev Use the development version of BioPerl from CVS
--bioperl_dev Use the development version of BioPerl from SVN
--gbrowse_dev Use the development version of GBrowse from CVS
--build_param_str=<args> Use this string to set Makefile.PL parameters
such as CONF or PREFIX for GBrowse
Expand Down Expand Up @@ -64,7 +63,7 @@ =head1 DESCRIPTION
use constant NMAKE => 'http://download.microsoft.com/download/vc15/patch/1.52/w95/en-us/nmake15.exe';

my ( $show_help, $get_from_cvs, $build_param_string, $working_dir,
$get_gbrowse_cvs, $get_bioperl_cvs, $is_cygwin, $windows,
$get_gbrowse_cvs, $get_bioperl_svn, $is_cygwin, $windows,
$binaries, $make, $tmpdir, $wincvs, $gbrowse_path,$bioperl_path,
$skip_start, $install_param_string, $skip_bioperl);

Expand All @@ -74,7 +73,7 @@ BEGIN
'h|help' => \$show_help, # Show help and exit
'd|dev' => \$get_from_cvs, # Use the dev cvs
'build_param_str=s' => \$build_param_string, # Build parameters
'bioperl_dev' => \$get_bioperl_cvs,
'bioperl_dev' => \$get_bioperl_svn,
'gbrowse_dev' => \$get_gbrowse_cvs,
'wincvs' => \$wincvs,
'gbrowse_path=s' => \$gbrowse_path,
Expand Down Expand Up @@ -161,7 +160,7 @@ BEGIN
$is_cygwin = 1 if ( $^O eq 'cygwin' );

if ($get_from_cvs) {
$get_bioperl_cvs = $get_gbrowse_cvs = 1;
$get_bioperl_svn = $get_gbrowse_cvs = 1;
}

if ($windows and !$wincvs and $get_gbrowse_cvs ) {
Expand All @@ -172,12 +171,12 @@ BEGIN
$build_param_string ||="";
$install_param_string ||="";

use constant BIOPERL_VERSION => 'bioperl-1.5.2_102';
use constant BIOPERL_REQUIRES => '1.005002'; # sorry for the redundancy
use constant BIOPERL_VERSION => 'bioperl-1.5.2_103';
use constant BIOPERL_REQUIRES => '1.005003'; # sorry for the redundancy
use constant BIOPERL_LIVE_URL => 'http://bioperl.org/DIST/nightly_builds/';
use constant GBROWSE_DEFAULT => '1.69';
use constant SOURCEFORGE_MIRROR1 => 'http://superb-west.dl.sourceforge.net/sourceforge/gmod/';
use constant SOURCEFORGE_MIRROR2 => 'http://easynews.dl.sourceforge.net/sourceforge/gmod/';
use constant SOURCEFORGE_MIRROR2 => 'http://superb-west.dl.sourceforge.net/sourceforge/gmod/';
use constant SOURCEFORGE_MIRROR1 => 'http://easynews.dl.sourceforge.net/sourceforge/gmod/';
use constant SOURCEFORGE_GBROWSE => 'http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=34513';
use constant BIOPERL => 'http://bioperl.org/DIST/'.BIOPERL_VERSION.'.tar.gz';

Expand Down Expand Up @@ -224,17 +223,24 @@ BEGIN
CPAN::Shell->install('Statistics::Descriptive');

unless ($skip_bioperl) {
$get_bioperl_cvs = 1;
$get_bioperl_svn = 1;
print STDERR "\n\nForce getting a BioPerl nightly build; the most recent release is too old\n";
my $version = BIOPERL_REQUIRES;
if (!(eval "use Bio::Perl $version; 1") or $get_bioperl_cvs or $bioperl_path) {
if (!(eval "use Bio::Perl $version; 1") or $get_bioperl_svn or $bioperl_path) {
print STDERR "\n*** Installing BioPerl ***\n";
if ($windows and !$get_bioperl_cvs and !$bioperl_path) {
if ($windows and !$get_bioperl_svn and !$bioperl_path) {
my $bioperl_index = find_bioperl_ppm();
system("ppm install --force $bioperl_index");
} else {
CPAN::Shell->install('Module::Build');
do_install(BIOPERL,'bioperl.tgz',BIOPERL_VERSION,'Build',$get_bioperl_cvs,'',$bioperl_path);
# recent versions of Module::Build fail to install without force!
CPAN::Shell->force('Module::Build') unless eval "require Module::Build; 1";
do_install(BIOPERL,
'bioperl.tgz',
BIOPERL_VERSION,
'Build',
$get_bioperl_svn ? 'svn' : '',
'',
$bioperl_path);
}
}
else {
Expand All @@ -246,7 +252,14 @@ BEGIN

my $latest_version = find_gbrowse_latest();
my $gbrowse = SOURCEFORGE_MIRROR1.$latest_version.'.tar.gz';
eval {do_install($gbrowse,'gbrowse.tgz',$latest_version,'make',$get_gbrowse_cvs,$build_param_string,$gbrowse_path,$install_param_string)};
eval {do_install($gbrowse,
'gbrowse.tgz',
$latest_version,
'make',
$get_gbrowse_cvs ? 'cvs' : '',
$build_param_string,
$gbrowse_path,
$install_param_string)};
if ($@ =~ /Could not download/) {
print STDERR "Could not download: server down? Trying a different server...\n";
$gbrowse = SOURCEFORGE_MIRROR2.$latest_version.'.tar.gz';
Expand All @@ -263,6 +276,7 @@ sub do_install {
my ($download,$local_name,$distribution,$method,
$from_cvs,$build_param_string,$file_path,$install_param_string) = @_;

$install_param_string ||= '';
chdir $tmpdir;

do_get_distro($download,$local_name,$distribution,$from_cvs,$file_path);
Expand All @@ -282,7 +296,7 @@ sub do_install {
}

sub do_get_distro {
my ($download,$local_name,$distribution,$from_cvs,$file_path) = @_;
my ($download,$local_name,$distribution,$distribution_method,$file_path) = @_;

if ($file_path) {
chdir $working_dir;
Expand All @@ -301,18 +315,18 @@ sub do_get_distro {
chdir $tmpdir;
extract_tarball($local_name,$distribution);
}
elsif ($from_cvs) {
elsif ($distribution_method) {
my $distribution_dir;
if ($local_name =~ /gbrowse/) {
$distribution_dir = 'Generic-Genome-Browser';
print STDERR "\n\nPlease press return when prompted for a password.\n";
unless (
(system(
'cvs -d:pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod login')==0
'$distribution_method -d:pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod login')==0
or $is_cygwin)
&&
(system(
'cvs -z3 -d:pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod co -kb -P -r stable Generic-Genome-Browser') == 0
'$distribution_method -z3 -d:pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod co -kb -P -r stable Generic-Genome-Browser') == 0
or $is_cygwin)
)
{
Expand Down

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