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CopyPeripheralGroupsResultsFromCache.pm
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53 lines (46 loc) · 4.49 KB
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package ApiCommonWorkflow::Main::WorkflowSteps::CopyPeripheralGroupsResultsFromCache;
@ISA = (ApiCommonWorkflow::Main::WorkflowSteps::WorkflowStep);
use strict;
use ApiCommonWorkflow::Main::WorkflowSteps::WorkflowStep;
sub run {
my ($self, $test, $undo) = @_;
my $preprocessedDataCache = $self->getSharedConfig('preprocessedDataCache');
my $workflowDataDir = $self->getWorkflowDataDir();
my $analysisDir = join("/", $workflowDataDir, $self->getParamValue("analysisDir"));
if ($undo) {
$self->runCmd(0, "echo 'undo'");
}
elsif ($test) {
$self->runCmd(0, "echo 'test'");
}
else {
# peripheralEntryResults
$self->runCmd(0, "mkdir -p $analysisDir/peripheralEntryResults/");
$self->runCmd(0, "cp -r ${preprocessedDataCache}/OrthoMCL/OrthoMCL_peripheralGroups/officialDiamondCache/peripherals.fasta $analysisDir/peripheralEntryResults/");
$self->runCmd(0, "cp -r ${preprocessedDataCache}/OrthoMCL/OrthoMCL_peripheralGroups/officialDiamondCache/intraGroupBlastFile.tsv $analysisDir/peripheralEntryResults/");
$self->runCmd(0, "cp -r ${preprocessedDataCache}/OrthoMCL/OrthoMCL_peripheralGroups/officialDiamondCache/coreBestReps.txt $analysisDir/peripheralEntryResults/");
$self->runCmd(0, "cp -r ${preprocessedDataCache}/OrthoMCL/OrthoMCL_peripheralGroups/officialDiamondCache/GroupsFile.txt $analysisDir/peripheralEntryResults/");
$self->runCmd(0, "cp -r ${preprocessedDataCache}/OrthoMCL/OrthoMCL_peripheralGroups/officialDiamondCache/peripheralCacheDir.tar.gz $analysisDir/peripheralEntryResults/");
$self->runCmd(0, "cp -r ${preprocessedDataCache}/OrthoMCL/OrthoMCL_peripheralGroups/officialDiamondCache/residuals.fasta $analysisDir/peripheralEntryResults/");
$self->runCmd(0, "cp -r ${preprocessedDataCache}/OrthoMCL/OrthoMCL_peripheralGroups/officialDiamondCache/groupStats $analysisDir/peripheralEntryResults/");
$self->runCmd(0, "cp -r ${preprocessedDataCache}/OrthoMCL/OrthoMCL_peripheralGroups/officialDiamondCache/residuals.fasta $analysisDir/peripheralEntryResults/");
$self->runCmd(0, "cp -r ${preprocessedDataCache}/OrthoMCL/OrthoMCL_peripheralGroups/officialDiamondCache/groupFastas $analysisDir/peripheralEntryResults/");
# postResidualEntryResults
$self->runCmd(0, "mkdir -p $analysisDir/postResidualEntryResults/");
$self->runCmd(0, "cp -r ${preprocessedDataCache}/OrthoMCL/OrthoMCL_peripheralGroups/officialDiamondCache/groupStats $analysisDir/postResidualEntryResults/");
$self->runCmd(0, "cp -r ${preprocessedDataCache}/OrthoMCL/OrthoMCL_peripheralGroups/officialDiamondCache/residualBestReps.txt $analysisDir/postResidualEntryResults/");
$self->runCmd(0, "cp -r ${preprocessedDataCache}/OrthoMCL/OrthoMCL_peripheralGroups/officialDiamondCache/residualGroupFastas $analysisDir/postResidualEntryResults/");
$self->runCmd(0, "cp -r ${preprocessedDataCache}/OrthoMCL/OrthoMCL_peripheralGroups/officialDiamondCache/residualBuildVersion.txt $analysisDir/postResidualEntryResults/");
$self->runCmd(0, "cp -r ${preprocessedDataCache}/OrthoMCL/OrthoMCL_peripheralGroups/officialDiamondCache/intraResidualGroupBlastFile.tsv $analysisDir/postResidualEntryResults/");
$self->runCmd(0, "cp -r ${preprocessedDataCache}/OrthoMCL/OrthoMCL_peripheralGroups/officialDiamondCache/reformattedGroups.txt $analysisDir/postResidualEntryResults");
# postProcessingEntryResults
$self->runCmd(0, "mkdir -p $analysisDir/postProcessingEntryResults/");
$self->runCmd(0, "cp -r ${preprocessedDataCache}/OrthoMCL/OrthoMCL_peripheralGroups/officialDiamondCache/bestRepsFull.fasta $analysisDir/postProcessingEntryResults/");
$self->runCmd(0, "cp -r ${preprocessedDataCache}/OrthoMCL/OrthoMCL_peripheralGroups/officialDiamondCache/fullGroupFile.txt $analysisDir/postProcessingEntryResults/");
$self->runCmd(0, "cp -r ${preprocessedDataCache}/OrthoMCL/OrthoMCL_peripheralGroups/officialDiamondCache/similar_groups.tsv $analysisDir/postProcessingEntryResults/");
$self->runCmd(0, "cp -r ${preprocessedDataCache}/OrthoMCL/OrthoMCL_peripheralGroups/officialDiamondCache/ortho*db.dmnd $analysisDir/postProcessingEntryResults/");
$self->runCmd(0, "cp -r ${preprocessedDataCache}/OrthoMCL/OrthoMCL_peripheralGroups/officialDiamondCache/previousGroups.txt $analysisDir/postProcessingEntryResults/");
$self->runCmd(0, "cp -r ${preprocessedDataCache}/OrthoMCL/OrthoMCL_peripheralGroups/officialDiamondCache/geneTrees $analysisDir/postProcessingEntryResults/");
}
}
1;