Imported Upstream version 3.6.3+dfsg
Sascha Steinbiss
7 years ago
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name = Bio-Roary
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version = 3.6.2
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version = 3.6.3
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author = Andrew J. Page <ap13@sanger.ac.uk>
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license = GPL_3
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copyright_holder = Wellcome Trust Sanger Institute
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has 'dont_delete_files' => ( is => 'rw', isa => 'Bool', default => 0 );
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has 'num_input_files' => ( is => 'ro', isa => 'Int', required => 1);
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# Overload Role
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# Overload Role`
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has 'memory_in_mb' => ( is => 'rw', isa => 'Int', lazy => 1, builder => '_build_memory_in_mb' );
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has '_min_memory_in_mb' => ( is => 'ro', isa => 'Int', default => 1500 );
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has '_max_memory_in_mb' => ( is => 'ro', isa => 'Int', default => 60000 );
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sub _build__files_per_chunk
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{
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my ($self) = @_;
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if($self->num_input_files > 1000)
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{
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return 5;
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}
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elsif($self->num_input_files > 500)
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{
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return 7;
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}
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return 10;
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return 1;
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}
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sub _build_memory_in_mb {
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use Moose;
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use File::Temp qw/ tempfile /;
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use Log::Log4perl qw(:easy);
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use File::Slurper 'write_text';
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use File::Temp qw/ tempfile /;
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has 'commands_to_run' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
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has 'cpus' => ( is => 'ro', isa => 'Int', default => 1 );
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sub run {
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my ($self) = @_;
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my($fh, $temp_command_filename) = tempfile();
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write_text($temp_command_filename, join("\n", @{ $self->commands_to_run }) );
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for my $command_to_run(@{ $self->commands_to_run })
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{
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$self->logger->info($command_to_run);
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}
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open(my $fh,"|-","parallel --gnu -j ".$self->cpus) || die "GNU Parallel failed";
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print $fh join("\n", @{ $self->commands_to_run });
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close $fh;
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my $parallel_command = "parallel --gnu -j ".$self->cpus." < ".$temp_command_filename ;
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$self->logger->info($parallel_command );
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system($parallel_command);
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1;
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}
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unlink($output_blast_results_filename) unless($self->dont_delete_files == 1);
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my $post_analysis = Bio::Roary::External::PostAnalysis->new(
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job_runner => $self->job_runner,
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job_runner => 'Local',
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cpus => $self->cpus,
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fasta_files => $self->fasta_files,
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input_files => $self->input_files,
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