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#!/usr/bin/perl
use strict;
use File::Basename qw( basename fileparse );
use Carp 'croak';
use IO::Dir;
use File::Path 'mkpath';
use Bio::Root::IO;
use Cwd;
use FindBin '$Bin';
my $origdir = cwd;
my $homedir = "$Bin/..";
chdir $homedir or die "couldn't cd to $homedir: $!\n";
foreach (@ARGV) {
$_ =~ s/^\"(.*)\"$/$1/;
}
my %options = map {split /=/} @ARGV;
my $root = $options{GBROWSE_ROOT} || 'gbrowse2';
my $ht_target = "$options{HTDOCS}/$root";
print "Installing stylesheet and images...\n";
if (! (-e $ht_target) ) {
mkpath($ht_target,0,0777) or die "unable to make $ht_target directory\n";
}
my $localreadmedir = ".";
opendir README, $localreadmedir or die "unable to opendir $localreadmedir\n";
while (my $file = readdir(README)) {
my $localfile = Bio::Root::IO->catfile($localreadmedir, $file);
if (-f $localfile and $file =~ /^README/) {
my $installfile = Bio::Root::IO->catfile($ht_target, $file);
chmod (0666, $installfile);
copy_with_substitutions($localfile, $installfile)
or die "unable to copy to $installfile\n";
chmod (0444, $installfile);
}
}
closedir README;
my $localhtdocsdir = "htdocs";
opendir HTDOCS, $localhtdocsdir or die "unable to opendir $localhtdocsdir\n";
while (my $file = readdir(HTDOCS) ) {
my $localfile = Bio::Root::IO->catfile($localhtdocsdir, $file);
if (-f $localfile) {
my $installfile = Bio::Root::IO->catfile($ht_target, $file);
chmod (0666, $installfile);
copy_with_substitutions($localfile, $installfile)
or die "unable to copy to $installfile\n";
chmod (0444, $installfile);
}
}
closedir HTDOCS;
my $imagedir = Bio::Root::IO->catfile($ht_target, "images");
my $buttondir = Bio::Root::IO->catfile($imagedir, "buttons");
my $balloondir = Bio::Root::IO->catfile($imagedir, "balloons");
my $jsdir = Bio::Root::IO->catfile($ht_target, "js");
for my $ddir ( $imagedir,$buttondir,$balloondir,$jsdir ) {
if (! (-e $ddir) ) {
print "Making $ddir...\n";
mkdir($ddir,0777) or die "unable to make $ddir\n";
}
}
my $localbuttondir = "htdocs/images/buttons";
opendir BUTTONS, $localbuttondir or die "unable to open $localbuttondir\n";
while (my $file = readdir(BUTTONS) ) {
my $localfile = Bio::Root::IO->catfile($localbuttondir,$file);
if (-f $localfile) {
my $installfile = Bio::Root::IO->catfile($buttondir, $file);
chmod (0666, $installfile);
copy_with_substitutions($localfile, $installfile)
or die "unable to copy to $installfile\n";
chmod (0444, $installfile);
}
}
closedir BUTTONS;
my $localballoondir = "htdocs/images/balloons";
opendir BALLOONS, $localballoondir or die "unable to open $localballoondir\n";
while (my $file = readdir(BALLOONS) ) {
my $localfile = Bio::Root::IO->catfile($localballoondir,$file);
if (-f $localfile) {
my $installfile = Bio::Root::IO->catfile($balloondir, $file);
chmod (0666, $installfile);
copy_with_substitutions($localfile, $installfile)
or die "unable to copy to $installfile\n";
chmod (0444, $installfile);
}
}
closedir BALLOONS;
my $helpdir = Bio::Root::IO->catfile($imagedir, "help");
if (! (-e $helpdir) ) {
print "Making $helpdir...\n";
mkdir($helpdir,0777) or die "unable to make $helpdir\n";
}
my $localhelpdir = "htdocs/images/help";
opendir HELP, $localhelpdir or die "unable to open $localhelpdir\n";
while (my $file = readdir(HELP) ) {
my $localfile = Bio::Root::IO->catfile($localhelpdir, $file);
if (-f "./htdocs/images/help/$file") {
my $installfile = Bio::Root::IO->catfile($helpdir, $file);
chmod (0666, $installfile);
copy_with_substitutions($localfile, $installfile)
or die "unable to copy to $installfile\n";
chmod (0444, $installfile);
}
}
closedir HELP;
print "Installing temporary directory...\n";
my $tmpdir = Bio::Root::IO->catfile($ht_target, "tmp");
if (! (-e $tmpdir) ) {
print "Making $tmpdir...\n";
mkdir($tmpdir,0777) or die "unable to make $tmpdir\n";
chmod 0777, $tmpdir or die "unable to make $tmpdir world writable\n";
}
print "Installing documentation...\n";
#this need to be replaced with:
# a pod2html dohicky (it can create the html in the htdocs dir directly)
# a wanted subroutine to do File::Find's work
# also need to modify gbrowse/index.html
for my $localfile ("DISCLAIMER") {
my $installfile = Bio::Root::IO->catfile($ht_target,basename($localfile));
chmod (0666, $installfile);
copy_with_substitutions($localfile,$installfile);
chmod(0444,$installfile);
}
#installing pod docs
my $docdir = Bio::Root::IO->catfile($ht_target, "docs");
if (! (-e $docdir) ) {
mkdir($docdir,0777) or die "unable to make $docdir\n";
}
my $poddir = Bio::Root::IO->catfile($docdir, "pod");
if (! (-e $poddir) ) {
mkdir($poddir,0777) or die "unable to make $poddir\n";
}
my $localpoddir = "docs/pod/";
my @localpodfiles = glob($localpoddir . "*.pod");
for my $localfile ( @localpodfiles ) {
my ($name,undef,undef) = fileparse($localfile, "\.pod");
my $installfile = Bio::Root::IO->catfile("$ht_target/docs/pod","$name.html");
system("pod2html", "--infile=$localfile",
"--outfile=$installfile",
"--htmlroot=/gbrowse",
"--htmldir=$ht_target ",
"--podpath=$localpoddir",
"--title=$name");
}
#get rid of pod2html junk
unlink './pod2htmi.x~~';
unlink './pod2htmd.x~~';
print "Installing tutorial...\n";
copy_tree("./docs/tutorial",$ht_target);
print "Installing sample_data...\n";
copy_tree("./sample_data",$ht_target);
print "Installing contrib...\n";
copy_tree("./contrib",$ht_target);
print "Installing js files...\n";
copy_tree("./htdocs/js",$ht_target);
print "Installing sample data files...\n";
copy_tree("./htdocs/databases",$ht_target);
chmod 0777,glob("$ht_target/databases/*");
print "\n\n#############################################################################\n";
print "GBrowse is now installed. Read INSTALL for further setup instructions.\n";
print "Go to http://localhost/$root for the online tutorial and reference manual.\n";
print "#############################################################################\n";
chdir $origdir or die "couldn't cd to $origdir: $!\n";
exit 0;
sub copy_tree {
my ($src,$dest) = @_;
if (-f $src) {
copy_with_substitutions($src,$dest) or die "copy_with_substitutions($src,$dest): $!";
return 1;
}
croak "$src doesn't exist" unless -e $src;
croak "Usage: copy_tree(\$src,\$dest). Can't copy a directory into a file or vice versa"
unless -d $src && -d $dest;
croak "Can't read from $src" unless -r $src;
croak "Can't write to $dest" unless -w $dest;
my $tgt = basename($src);
# create the dest if it doesn't exist
mkdir ("$dest/$tgt",0777) or die "mkdir($dest/$tgt): $!" unless -d "$dest/$tgt";
my $d = IO::Dir->new($src) or die "opendir($src): $!";
while (my $item = $d->read) {
# bunches of things to skip
next if $item eq 'CVS';
next if $item =~ /^\./;
next if $item =~ /~$/;
next if $item =~ /^\#/;
if (-f "$src/$item") {
copy_with_substitutions("$src/$item","$dest/$tgt") or die "copy_with_substitutions('$src/$item','$dest/$tgt'): $!";
} elsif (-d "$src/$item") {
copy_tree("$src/$item","$dest/$tgt");
}
}
1;
}
sub copy_with_substitutions {
my ($localfile,$install_file) = @_;
open (IN,$localfile) or warn "Couldn't open $localfile: $!";
my $basename = basename($localfile);
my $dest = -d $install_file ? "$install_file/$basename" : $install_file;
open (OUT,">$dest") or die "Couldn't open $install_file for writing: $!";
if (-T IN) {
while (<IN>) {
s/\$(\w+)/$options{$1}||"\$$1"/eg;
print OUT;
}
}
else {
binmode IN;
binmode OUT;
my $buffer;
print OUT $buffer while read(IN,$buffer,5000);
}
close OUT;
close IN;
}
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