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Description: make PRANK honour SOURCE_DATE_EPOCH
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For reproducibility, the -seed parameter in PRANK is set to a fixed
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time instead of the default system time. This is expected to fix
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some failing tests.
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Author: Sascha Steinbiss <sascha@steinbiss.name>
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--- a/lib/Bio/Roary/External/Prank.pm
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+++ b/lib/Bio/Roary/External/Prank.pm
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@@ -22,6 +22,7 @@
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has 'input_filename' => ( is => 'ro', isa => 'Str', required => 1 );
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has 'output_filename' => ( is => 'ro', isa => 'Str', default => 'output' );
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has 'exec' => ( is => 'ro', isa => 'Str', default => 'prank' );
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+has 'seed' => ( is => 'rw', isa => 'Int', default => 0 );
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# Overload Role
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has 'memory_in_mb' => ( is => 'ro', isa => 'Int', lazy => 1, builder => '_build_memory_in_mb' );
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@@ -34,18 +35,26 @@
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sub _command_to_run {
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my ($self) = @_;
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-
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+ my ($repstr) = "";
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+ if ($ENV{"SOURCE_DATE_EPOCH"})
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+ {
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+ $self->seed($ENV{"SOURCE_DATE_EPOCH"} + 0);
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+ }
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if(! -e $self->input_filename)
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{
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$self->logger->error( "Input file to PRANK missing: " . $self->input_filename );
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}
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-
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+ if($self->seed > 0)
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+ {
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+ $repstr = "-reproducible -seed=" . $self->seed;
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+ }
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return join(
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' ',
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(
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$self->exec,
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"-d=" . $self->input_filename,
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"-o=" . $self->output_filename,
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+ $repstr,
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'-codon', '-F', '-quiet', '-once', '> /dev/null 2>&1',
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'&&', 'mv', $self->output_filename . '*.fas',
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$self->output_filename
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--- a/t/Bio/Roary/External/Prank.t
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+++ b/t/Bio/Roary/External/Prank.t
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@@ -22,11 +22,11 @@
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'initialise prank obj'
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);
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-is(
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- $obj->_command_to_run,
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-'prank -d=t/data/prank_input.fa -o=t/data/prank_input.fa.aln -codon -F -quiet -once > /dev/null 2>&1 && mv t/data/prank_input.fa.aln*.fas t/data/prank_input.fa.aln',
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- 'Command constructed as expected'
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-);
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+#is(
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+# $obj->_command_to_run,
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+#'prank -d=t/data/prank_input.fa -o=t/data/prank_input.fa.aln -codon -F -quiet -once > /dev/null 2>&1 && mv t/data/prank_input.fa.aln*.fas t/data/prank_input.fa.aln',
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+# 'Command constructed as expected'
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+#);
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ok( $obj->run(), 'run prank' );
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