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GMOD/Admin/Update.pm view on Meta::CPAN
my $method = $sync_to . "_version";
my $version = $self->$method || 'unknown_version';
$tmp_path ||= $adaptor->tmp_path;
my $full_path = "$tmp_path/$version";
unless (-e "$full_path") {
$self->logit(-msg => "Creating temporary directory at $full_path");
my $command = <<END;
mkdir -p $full_path
chmod -R 0775 $full_path
END
;
my $result = system($command);
if ($result == 0) {
$self->logit(-msg => "Successfully created temporary directory");
} else {
$self->logit(-msg => "Cannot make temporary directory: $!",
-die => 1);
}
}
GMOD/Admin/Update/WormBase.pm view on Meta::CPAN
$self->logit(-msg => "Unpacking and installing $acedb");
chdir($acedb_path);
system("gunzip -c $local_path/$acedb | tar -x --no-same-owner -f -");
unlink($acedb_path . '/elegans');
symlink("elegans_$version",'elegans');
# Adjust permissions
my $command = <<END;
chown -R acedb $acedb_path/elegans*
chgrp -R acedb $acedb_path/elegans*
chmod 2775 $acedb_path/elegans*
##chown acedb $acedb_path/bin/*
##chgrp acedb $acedb_path/bin/*
END
$self->test_for_error(system($command),"Fetching and installing acedb for WormBase");
}
}
sub fetch_elegans_gff {
GMOD/Admin/Update/WormBase.pm view on Meta::CPAN
# Create the blast directory
mkdir blast
gunzip -c $local_path/$blast | tar -x --no-same-owner -f -
mv blast_$version blast/.
rm -f blast/blast
cd blast/
ln -s blast_$version blast
# Fix permissions as necessary
chgrp -R wormbase /usr/local/wormbase/blat
chmod 2775 /usr/local/wormbase/blat
END
$self->test_for_error(system($command),"Fetching and installing blast databases for WormBase");
}
}
sub fetch_briggsae_gff {
my ($self,@p) = @_;
GMOD/Util/Mirror.pm view on Meta::CPAN
my ($lsize,$ltime) = stat($path) ? (stat(_))[7,9] : (0,0);
if ( defined($rtime) and defined($rsize)
and ($ltime >= $rtime)
and ($lsize == $rsize) ) {
$self->warning(-msg => "Getting file $path: not newer than local copy.") if $self->verbose;
return 1;
}
$self->logit(-msg => "Downloading file $path");
$ftp->get($path) or ($self->warning(-msg=>$ftp->message) and return);
chmod $mode,$path if $mode;
}
# mirror a directory, recursively
sub get_dir {
my $self = shift;
my ($path,$mode) = @_;
my $localpath = $path;
-d $localpath or mkpath $localpath or carp "mkpath failed: $!" && return;
chdir $localpath or carp "can't chdir to $localpath: $!" && return;
$mode = 0755 if ($mode == 365); # Kludge-can't mirror non-writable directories
chmod $mode,'.' if $mode;
my $ftp = $self->ftp;
my $cwd = $ftp->pwd or carp("can't pwd: ",$ftp->message) && return;
$ftp->cwd($path) or carp("can't cwd: ",$ftp->message) && return;
$self->logit(-msg => "Downloading directory $path") if $self->verbose;
foreach ($ftp->dir) {
next unless my ($type,$name,$mode) = $self->parse_listing($_);
bin/gmod_check_versions.PLS view on Meta::CPAN
my $hash = shift;
print "Status : $hash->{status}\n";
print "Title : $hash->{name}\n";
print "Version : $hash->{version}\n";
print "Released : $hash->{released}\n\n";
}
!NO!SUBS!
close OUT or die "Can't close $file: $!";
chmod 0755, $file or die "Can't reset permissions for $file: $!\n";
exec("$Config{'eunicefix'} $file") if $Config{'eunicefix'} ne ':';
chdir $origdir;
bin/gmod_fetch_genes.PLS view on Meta::CPAN
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
=cut
!NO!SUBS!
close OUT or die "Can't close $file: $!";
chmod 0755, $file or die "Can't reset permissions for $file: $!\n";
exec("$Config{'eunicefix'} $file") if $Config{'eunicefix'} ne ':';
chdir $origdir;
bin/gmod_monitor_installation-wormbase.PLS view on Meta::CPAN
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
=cut
!NO!SUBS!
close OUT or die "Can't close $file: $!";
chmod 0755, $file or die "Can't reset permissions for $file: $!\n";
exec("$Config{'eunicefix'} $file") if $Config{'eunicefix'} ne ':';
chdir $origdir;
bin/gmod_monitor_installation.PLS view on Meta::CPAN
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
=cut
!NO!SUBS!
close OUT or die "Can't close $file: $!";
chmod 0755, $file or die "Can't reset permissions for $file: $!\n";
exec("$Config{'eunicefix'} $file") if $Config{'eunicefix'} ne ':';
chdir $origdir;
bin/gmod_standard_urls.PLS view on Meta::CPAN
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
=cut
!NO!SUBS!
close OUT or die "Can't close $file: $!";
chmod 0755, $file or die "Can't reset permissions for $file: $!\n";
exec("$Config{'eunicefix'} $file") if $Config{'eunicefix'} ne ':';
chdir $origdir;
bin/gmod_update_installation-wormbase.PLS view on Meta::CPAN
Copyright (c) 2004-2005 Cold Spring Harbor Laboratory.
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
=cut
!NO!SUBS!
close OUT or die "Can't close $file: $!";
chmod 0755, $file or die "Can't reset permissions for $file: $!\n";
exec("$Config{'eunicefix'} $file") if $Config{'eunicefix'} ne ':';
chdir $origdir;
bin/gmod_update_installation.PLS view on Meta::CPAN
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
=cut
!NO!SUBS!
close OUT or die "Can't close $file: $!";
chmod 0755, $file or die "Can't reset permissions for $file: $!\n";
exec("$Config{'eunicefix'} $file") if $Config{'eunicefix'} ne ':';
chdir $origdir;
cgi-bin/defaults.wormbase.PLS view on Meta::CPAN
CURRENT_RELEASE=/pub/wormbase/elegans-current_release
ARCHIVE_PATH=/usr/local/ftp/pub/wormbase/database_tarballs
ARCHIVE_REPOSITORY=/pub/wormbase/archive
END
exit 0;
!NO!SUBS!
close OUT or die "Can't close $file: $!\n";
chmod 0755, $file or die "Can't reset permissions for $file: $!\n";
exec("$Config{'eunicefix'} $file") if $Config{'eunicefix'} ne ':';
chdir $origdir;
cgi-bin/version.wormbase.PLS view on Meta::CPAN
print "<mod_version>\n";
print "<name>WormBase</name>\n";
print "<description>$title</description>\n";
print "<version>$version</version>\n";
print "<release_date>$modtime</release_date>\n";
print "</mod_version>";
exit 0;
!NO!SUBS!
close OUT or die "Can't close $file: $!";
chmod 0755, $file or die "Can't reset permissions for $file: $!\n";
exec("$Config{'eunicefix'} $file") if $Config{'eunicefix'} ne ':';
chdir $origdir;
install_util/cgi_install.PLS view on Meta::CPAN
next if /~$/;
next if /\.PLS$/;
next unless (-f $_);
next unless /$mod$/i;
my $install_target = $_;
$install_target =~ s/\.$mod//i;
my $installfile = Bio::Root::IO->catfile($cgi_target, $install_target);
warn "copying $_ to $installfile\n";
copy($_, $installfile ) or die "unable to copy to $installfile\n";
my $mode = 0755;
chmod $mode, $installfile
or die "unable to make $installfile world executable\n";
}
chdir $origdir or die "couldn't cd to $origdir: $!\n";
!NO!SUBS!
close OUT or die "Can't close $file: $!";
chmod 0755, $file or die "Can't reset permissions for $file: $!\n";
exec("$Config{'eunicefix'} $file") if $Config{'eunicefix'} ne ':';
chdir $origdir;
install_util/conf_install.PLS view on Meta::CPAN
}
opendir(my $SOURCE, $source) or die "unable to opendir('$source'): $!";
while(my $file = readdir($SOURCE)){
next if $file =~ /\.PMS$/;
my $sourcefile = Bio::Root::IO->catfile($source,$file);
my $targetfile = Bio::Root::IO->catfile($target,$file);
if(-f $sourcefile){
chmod(0666,$targetfile);
# copy($sourcefile,$targetfile) or die "unable to write to $targetfile: $!";
copy_with_substitutions($sourcefile,$targetfile) or die "unable to write to $targetfile: $!";
print STDERR " file $sourcefile -> $targetfile\n" if DEBUG;
chmod(0444,$targetfile);
} elsif(-d $sourcefile && $recurse){
next if $file eq '.' or $file eq '..' or $file eq 'CVS';
print STDERR "directory $sourcefile -> $targetfile\n" if DEBUG;
installdir(source => $sourcefile, target => $targetfile, recurse => 1);
}
}
closedir($SOURCE);
}
sub copy_with_substitutions {
install_util/conf_install.PLS view on Meta::CPAN
s/\$(\w+)/$options{$1}||"\$$1"/eg;
print OUT;
}
close OUT;
close IN;
}
chdir $origdir or die "couldn't cd to $origdir: $!\n";
!NO!SUBS!
close OUT or die "Can't close $file: $!";
chmod 0755, $file or die "Can't reset permissions for $file: $!\n";
exec("$Config{'eunicefix'} $file") if $Config{'eunicefix'} ne ':';
chdir $origdir;
install_util/gbrowse_ppm_install.PLS view on Meta::CPAN
s/^\#!.+/$startperl -w/;
s/^\$CONF_DIR\s*=\s*\'.+/\$CONF_DIR = '$conf';/;
print OUT $_,"\n";
}
close F;
close OUT;
rename "$file.new",$file;
}
!NO!SUBS!
close OUT or die "Can't close $file: $!";
chmod 0755, $file or die "Can't reset permissions for $file: $!\n";
exec("$Config{'eunicefix'} $file") if $Config{'eunicefix'} ne ':';
install_util/htdocs_install.PLS view on Meta::CPAN
if (! (-e $ht_target) ) {
mkpath($ht_target,0,0777) or die "unable to make $ht_target directory\n";
}
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");
if (! (-e $imagedir) ) {
print "Making $imagedir...\n";
mkdir($imagedir,0777) or die "unable to make $imagedir\n";
}
install_util/htdocs_install.PLS view on Meta::CPAN
print "Making $buttondir...\n";
mkdir($buttondir,0777) or die "unable to make $buttondir\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 $helpdir = Bio::Root::IO->catfile($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 $poddir\n";
install_util/htdocs_install.PLS view on Meta::CPAN
copy_tree("./docs/tutorial",$ht_target);
print "Installing sample_data...\n";
copy_tree("./sample_data",$ht_target);
print "Installing contrib...\n";
copy_tree("./contrib",$ht_target);
print "Installing 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/gbrowse/ 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 {
install_util/htdocs_install.PLS view on Meta::CPAN
binmode OUT;
my $buffer;
print OUT $buffer while read(IN,$buffer,5000);
}
close OUT;
close IN;
}
!NO!SUBS!
close OUT or die "Can't close $file: $!";
chmod 0755, $file or die "Can't reset permissions for $file: $!\n";
exec("$Config{'eunicefix'} $file") if $Config{'eunicefix'} ne ':';
chdir $origdir;