Bio-Grid-Run-SGE
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lib/Bio/Grid/Run/SGE/Master.pm view on Meta::CPAN
@inc_dirs = grep {$_} @inc_dirs;
if ( @inc_dirs && @inc_dirs > 0 ) {
say $fh '$ENV{PERL5LIB} //= "";';
say $fh '$ENV{PERL5LIB} = "$ENV{PERL5LIB}:' . join( ':', @inc_dirs ) . '";';
say $fh "use lib ('" . join( "','", @inc_dirs ) . "');";
}
}
if ( exists $ENV{PATH} ) {
my @dirs = uniq( grep {$_} split( /\Q$Config{path_sep}\E/, $ENV{PATH} ) );
my $path = "'" . join( "','", @dirs ) . "'";
print $fh <<EOS;
my \@path = do { my \%seen; grep { !\$seen{\$_}++ } ( $path, split(/:/, \$ENV{PATH})) };
\$ENV{PATH} = join(":", \@path);
EOS
}
print $fh <<'EOF';
my $cmd = shift;
unless ( my $return = do $cmd ) {
warn "could not parse $cmd\n$@\n\n$!" if $@;
warn "couldn't execute $cmd\n$!" unless defined $return;
warn "couldn't run $cmd" unless $return;
}
exit;
EOF
$fh->close;
}
sub queue_post_task {
my ($self) = @_;
my $conf = $self->config;
my $env = $self->env;
my @cmd = ( $conf->{submit_bin} );
push @cmd, '-S', $env->{perl_bin};
push @cmd, '-N', join( '_', 'p' . $env->{job_id}, $env->{job_name_save} );
push @cmd, '-e', $conf->{stderr_dir};
push @cmd, '-o', $conf->{stdout_dir};
my @hold_arg = ( '-hold_jid', $env->{job_id} );
#push @cmd, @{ $self->submit_params };
my @post_cmd = (
$env->{worker_env_script},
$env->{script_bin}, '--stage', 'post_task', '--job_id', $env->{job_id}, $env->{worker_config_file}
);
$self->log->info( "post processing: " . join( " ", @cmd, @hold_arg, @post_cmd ) );
my $post_cmd_file
= catfile( $conf->{tmp_dir}, sprintf( "post.%s.j%s.cmd", $env->{job_name_save}, $env->{job_id} ) );
open my $post_fh, '>', $post_cmd_file or confess "Can't open filehandle: $!";
say $post_fh join( " ", "cd", "'" . fastcwd . "'", '&&', @cmd, @post_cmd );
$post_fh->close;
chmod 0755, $post_cmd_file;
system( @cmd, @hold_arg, @post_cmd ) == 0 or confess "post task system failed: $?";
return;
}
1;
__END__
=head1 NAME
=head1 SYNOPSIS
#wenn export, dann hier im qw()
=head1 DESCRIPTION
=over 4
=item B<< combinations_per_task >>
=item B<< num_parts >>
=back
=head1 OPTIONS
=head1 SUBROUTINES
=head1 METHODS
=head1 SEE ALSO
=head1 AUTHOR
jw bargsten, C<< <jwb at cpan dot org> >>
=cut
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