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changes for better cluster orchestration #26

Merged
merged 18 commits into from
Dec 20, 2024
Merged

changes for better cluster orchestration #26

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7aa9b56
copy nextflow.txt back to reflow server
jbrestel Nov 21, 2024
7004c82
Merge branch 'webdb_workflow' into cluster_orchestration
jbrestel Dec 3, 2024
8535ed6
remove unused ms from mgf graph
jbrestel Dec 3, 2024
91e4c50
delete unused graphs
jbrestel Dec 4, 2024
df70e22
Merge branch 'webdb_workflow' into cluster_orchestration
jbrestel Dec 6, 2024
5e6b7b1
Merge branch 'webdb_workflow' into cluster_orchestration
jbrestel Dec 10, 2024
0a2d82b
add proteomes and other missing dependencies for symlinnk dependent d…
jbrestel Dec 11, 2024
2e435d9
add missing dependency
jbrestel Dec 11, 2024
9b0ef0d
Merge branch 'webdb_workflow' into cluster_orchestration
jbrestel Dec 11, 2024
0f44808
symlink dependent data for genome analyses
jbrestel Dec 11, 2024
d069a90
Merge branch 'webdb_workflow' into cluster_orchestration
jbrestel Dec 11, 2024
90b827e
use cluster temp dir for next flow data
steve-fischer-200 Dec 12, 2024
9299c5b
move sub to superclass
steve-fischer-200 Dec 12, 2024
6eb6a15
wip
steve-fischer-200 Dec 13, 2024
8e73c09
debug
steve-fischer-200 Dec 17, 2024
a37cff0
remove mirror
steve-fischer-200 Dec 19, 2024
d4234aa
remove mirror
steve-fischer-200 Dec 19, 2024
68ab183
Merge pull request #30 from VEuPathDB/cluster_rel_paths
jbrestel Dec 20, 2024
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11 changes: 8 additions & 3 deletions Main/lib/perl/WorkflowSteps/MakeBlastPPdbNextflowConfig.pm
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Expand Up @@ -22,6 +22,7 @@ sub run {
my $nextflowConfigFile = $self->getParamValue("nextflowConfigFile");
my $resultsDirectory = $self->getParamValue("resultsDirectory");
my $outputFileName = $self->getParamValue("outputFileName");
my $workingDirRelativePath = $self->getParamValue("workingDirRelativePath");

my $workflowDataDir = $self->getWorkflowDataDir();

Expand All @@ -38,14 +39,18 @@ sub run {
my $nextflowConfig = "$workflowDataDir/$nextflowConfigFile";
open(F, ">$nextflowConfig") || die "Can't open task prop file '$nextflowConfig' for writing";

my $proteinSequenceFileInNextflowWorkingDirOnCluster = $self->relativePathToNextflowClusterPath($workingDirRelativePath, $proteinSequenceFile);
my $pdbFastaFileInNextflowWorkingDirOnCluster = $self->relativePathToNextflowClusterPath($workingDirRelativePath, $pdbFastaFile);
my $resultsDirectoryInNextflowWorkingDirOnCluster = $self->relativePathToNextflowClusterPath($workingDirRelativePath, $resultsDirectory);

my $configString = <<NEXTFLOW;
params {
queryFastaFile = "$clusterWorkflowDataDir/$proteinSequenceFile"
outputDir = "$clusterWorkflowDataDir/$resultsDirectory"
queryFastaFile = "$proteinSequenceFileInNextflowWorkingDirOnCluster"
outputDir = "$resultsDirectoryInNextflowWorkingDirOnCluster"
outputFile = "$outputFileName"
fastaSubsetSize = $fastaSubsetSize
blastProgram = "blastp"
targetFastaFile = "$clusterWorkflowDataDir/$pdbFastaFile"
targetFastaFile = "$pdbFastaFileInNextflowWorkingDirOnCluster"
preConfiguredDatabase = false
targetDatabaseIndex = "NA"
}
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10 changes: 7 additions & 3 deletions Main/lib/perl/WorkflowSteps/MakeBlatNextflowConfig.pm
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Expand Up @@ -23,6 +23,7 @@ sub run {
my $dbType = $self->getParamValue("dbType");
my $queryType = $self->getParamValue("queryType");
my $outputFileName = $self->getParamValue("outputFileName");
my $workingDirRelativePath = $self->getParamValue("workingDirRelativePath");

my $increasedMemory = $self->getParamValue("increasedMemory");
my $initialMemory = $self->getParamValue("initialMemory");
Expand All @@ -41,15 +42,18 @@ sub run {
} else {
open(F, ">", $configPath) or die "$! :Can't open config file '$configPath' for writing";

my $queryFileInNextflowWorkingDirOnCluster = $self->relativePathToNextflowClusterPath($workingDirRelativePath, $seqFile);
my $databaseInNextflowWorkingDirOnCluster = $self->relativePathToNextflowClusterPath($workingDirRelativePath, $databasePath);
my $resultsDirectoryInNextflowWorkingDirOnCluster = $self->relativePathToNextflowClusterPath($workingDirRelativePath, $resultsDirectory);

my $configString = <<NEXTFLOW;
params {
queryFasta = "$seqFile"
queryFasta = "$queryFileInNextflowWorkingDirOnCluster"
fastaSubsetSize = $fastaSubsetSize
genomeFasta = "$databasePath"
genomeFasta = "$databaseInNextflowWorkingDirOnCluster"
dbType = "$dbType"
queryType = "$queryType"
outputDir = "$outputDir"
outputDir = "$resultsDirectoryInNextflowWorkingDirOnCluster"
outputFileName = "$outputFileName"
}

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11 changes: 8 additions & 3 deletions Main/lib/perl/WorkflowSteps/MakeEpitopeMappingNextflowConfig.pm
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Expand Up @@ -31,6 +31,7 @@ sub run {
my $peptideMatchResults = $self->getParamValue("peptideMatchResults");

my $nextflowConfigFile = $self->getParamValue("nextflowConfigFile");
my $workingDirRelativePath = $self->getParamValue("workingDirRelativePath");

my $clusterWorkflowDataDir = $self->getClusterWorkflowDataDir();
my $executor = $self->getClusterExecutor();
Expand All @@ -42,13 +43,17 @@ sub run {
my $nextflowConfig = "$workflowDataDir/$nextflowConfigFile";
open(F, ">$nextflowConfig") || die "Can't open task prop file '$nextflowConfig' for writing";

my $proteinSequenceFileInNextflowWorkingDirOnCluster = $self->relativePathToNextflowClusterPath($workingDirRelativePath, $proteinSequenceFile);
my $iedbPeptidesTabFileInNextflowWorkingDirOnCluster = $self->relativePathToNextflowClusterPath($workingDirRelativePath, $iedbPeptidesTabFile);
my $resultsDirectoryInNextflowWorkingDirOnCluster = $self->relativePathToNextflowClusterPath($workingDirRelativePath, $resultsDirectory);

my $configString = <<NEXTFLOW;
params {
refFasta = "$clusterWorkflowDataDir/$proteinSequenceFile"
peptidesTab = "$clusterWorkflowDataDir/$iedbPeptidesTabFile"
refFasta = "$proteinSequenceFileInNextflowWorkingDirOnCluster"
peptidesTab = "$iedbPeptidesTabFileInNextflowWorkingDirOnCluster"
taxon = $speciesNcbiTaxonId
peptideMatchResults = "$peptideMatchResults"
results = "$clusterWorkflowDataDir/$resultsDirectory"
results = "$resultsDirectoryInNextflowWorkingDirOnCluster"
nonTaxaShortPeptideCutoff = $nonTaxaShortPeptideCutoff
}
process {
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7 changes: 5 additions & 2 deletions Main/lib/perl/WorkflowSteps/MakeExportpredNextflowConfig.pm
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Expand Up @@ -14,6 +14,7 @@ sub run {
my $nextflowConfigFile = $self->getParamValue("nextflowConfigFile");
my $resultsDirectory = $self->getParamValue("resultsDirectory");
my $outputFileName = $self->getParamValue("outputFileName");
my $workingDirRelativePath = $self->getParamValue("workingDirRelativePath");

my $workflowDataDir = $self->getWorkflowDataDir();

Expand All @@ -27,11 +28,13 @@ sub run {
} else {
my $nextflowConfig = "$workflowDataDir/$nextflowConfigFile";
open(F, ">$nextflowConfig") || die "Can't open task prop file '$nextflowConfig' for writing";
my $proteinSequenceFileInNextflowWorkingDirOnCluster = $self->relativePathToNextflowClusterPath($workingDirRelativePath, $proteinSequenceFile);
my $resultsDirectoryInNextflowWorkingDirOnCluster = $self->relativePathToNextflowClusterPath($workingDirRelativePath, $resultsDirectory);

my $configString = <<NEXTFLOW;
params {
inputFilePath = "$clusterWorkflowDataDir/$proteinSequenceFile"
outputDir = "$clusterWorkflowDataDir/$resultsDirectory"
inputFilePath = "$proteinSequenceFileInNextflowWorkingDirOnCluster"
outputDir = "$resultsDirectoryInNextflowWorkingDirOnCluster"
outputFileName = "$outputFileName"
fastaSubsetSize = $fastaSubsetSize
}
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7 changes: 5 additions & 2 deletions Main/lib/perl/WorkflowSteps/MakeOrfFinderConfig.pm
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Expand Up @@ -15,6 +15,7 @@ sub run {
my $resultsDirectory = $self->getParamValue("resultsDirectory");
my $outputFileName = $self->getParamValue("outputFileName");
my $minPepLength = $self->getParamValue("minPepLength");
my $workingDirRelativePath = $self->getParamValue("workingDirRelativePath");

my $workflowDataDir = $self->getWorkflowDataDir();

Expand All @@ -29,11 +30,13 @@ sub run {
} else {
my $nextflowConfig = "$workflowDataDir/$nextflowConfigFile";
open(F, ">$nextflowConfig") || die "Can't open task prop file '$nextflowConfig' for writing";
my $genomicSequenceFileInNextflowWorkingDirOnCluster = $self->relativePathToNextflowClusterPath($workingDirRelativePath, $genomicSequenceFile);
my $resultsDirectoryInNextflowWorkingDirOnCluster = $self->relativePathToNextflowClusterPath($workingDirRelativePath, $resultsDirectory);

my $configString = <<NEXTFLOW;
params {
inputFilePath = "$clusterWorkflowDataDir/$genomicSequenceFile"
outputDir = "$clusterWorkflowDataDir/$resultsDirectory"
inputFilePath = "$genomicSequenceFileInNextflowWorkingDirOnCluster"
outputDir = "$resultsDirectoryInNextflowWorkingDirOnCluster"
outputFileName = "$outputFileName"
minPepLength = $minPepLength
fastaSubsetSize = $fastaSubsetSize
Expand Down
8 changes: 6 additions & 2 deletions Main/lib/perl/WorkflowSteps/MakeProteinAttributesNextflowConfig.pm
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Expand Up @@ -14,6 +14,7 @@ sub run {
my $nextflowConfigFile = $self->getParamValue("nextflowConfigFile");
my $resultsDirectory = $self->getParamValue("resultsDirectory");
my $outputFileName = $self->getParamValue("outputFileName");
my $workingDirRelativePath = $self->getParamValue("workingDirRelativePath");

my $workflowDataDir = $self->getWorkflowDataDir();

Expand All @@ -29,10 +30,13 @@ sub run {
my $nextflowConfig = "$workflowDataDir/$nextflowConfigFile";
open(F, ">$nextflowConfig") || die "Can't open task prop file '$nextflowConfig' for writing";

my $proteinSequenceFileInNextflowWorkingDirOnCluster = $self->relativePathToNextflowClusterPath($workingDirRelativePath, $proteinSequenceFile);
my $resultsDirectoryInNextflowWorkingDirOnCluster = $self->relativePathToNextflowClusterPath($workingDirRelativePath, $resultsDirectory);

my $configString = <<NEXTFLOW;
params {
inputFilePath = "$clusterWorkflowDataDir/$proteinSequenceFile"
outputDir = "$clusterWorkflowDataDir/$resultsDirectory"
inputFilePath = "$proteinSequenceFileInNextflowWorkingDirOnCluster"
outputDir = "$resultsDirectoryInNextflowWorkingDirOnCluster"
outputFileName = "$outputFileName"
fastaSubsetSize = $fastaSubsetSize
}
Expand Down
7 changes: 5 additions & 2 deletions Main/lib/perl/WorkflowSteps/MakePsiPredNextflowConfig.pm
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Expand Up @@ -19,6 +19,7 @@ sub run {
my $nextflowConfigFile = $self->getParamValue("nextflowConfigFile");
my $resultsDirectory = $self->getParamValue("resultsDirectory");
my $outputFilePrefix = $self->getParamValue("outputFilePrefix");
my $workingDirRelativePath = $self->getParamValue("workingDirRelativePath");

my $executor = $self->getClusterExecutor();
my $clusterConfigFile = "\$baseDir/conf/${executor}.config";
Expand All @@ -30,10 +31,12 @@ sub run {
my $nextflowConfig = "$workflowDataDir/$nextflowConfigFile";
open(F, ">$nextflowConfig") || die "Can't open task prop file '$nextflowConfig' for writing";

my $proteinSequenceFileInNextflowWorkingDirOnCluster = $self->relativePathToNextflowClusterPath($workingDirRelativePath, $proteinSequenceFile);
my $resultsDirectoryInNextflowWorkingDirOnCluster = $self->relativePathToNextflowClusterPath($workingDirRelativePath, $resultsDirectory);
my $configString = <<NEXTFLOW;
params {
inputFilePath = "$clusterWorkflowDataDir/$proteinSequenceFile"
outputDir = "$clusterWorkflowDataDir/$resultsDirectory"
inputFilePath = "$proteinSequenceFileInNextflowWorkingDirOnCluster"
outputDir = "$resultsDirectoryInNextflowWorkingDirOnCluster"
outputFilePrefix = "$outputFilePrefix"
fastaSubsetSize = $fastaSubsetSize
}
Expand Down
8 changes: 6 additions & 2 deletions Main/lib/perl/WorkflowSteps/MakeSegNextflowConfig.pm
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Expand Up @@ -14,6 +14,7 @@ sub run {
my $nextflowConfigFile = $self->getParamValue("nextflowConfigFile");
my $resultsDirectory = $self->getParamValue("resultsDirectory");
my $outputFileName = $self->getParamValue("outputFileName");
my $workingDirRelativePath = $self->getParamValue("workingDirRelativePath");

my $workflowDataDir = $self->getWorkflowDataDir();

Expand All @@ -29,10 +30,13 @@ sub run {
my $nextflowConfig = "$workflowDataDir/$nextflowConfigFile";
open(F, ">$nextflowConfig") || die "Can't open task prop file '$nextflowConfig' for writing";

my $proteinSequenceFileInNextflowWorkingDirOnCluster = $self->relativePathToNextflowClusterPath($workingDirRelativePath, $proteinSequenceFile);
my $resultsDirectoryInNextflowWorkingDirOnCluster = $self->relativePathToNextflowClusterPath($workingDirRelativePath, $resultsDirectory);

my $configString = <<NEXTFLOW;
params {
inputFilePath = "$clusterWorkflowDataDir/$proteinSequenceFile"
outputDir = "$clusterWorkflowDataDir/$resultsDirectory"
inputFilePath = "$proteinSequenceFileInNextflowWorkingDirOnCluster"
outputDir = "$resultsDirectoryInNextflowWorkingDirOnCluster"
outputFileName = "$outputFileName"
fastaSubsetSize = $fastaSubsetSize
seqType = "aa"
Expand Down
7 changes: 5 additions & 2 deletions Main/lib/perl/WorkflowSteps/MakeTRNAScanConfig.pm
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Expand Up @@ -14,6 +14,7 @@ sub run {
my $nextflowConfigFile = $self->getParamValue("nextflowConfigFile");
my $resultsDirectory = $self->getParamValue("resultsDirectory");
my $trnascanOutputFileName = $self->getParamValue("outputFileName");
my $workingDirRelativePath = $self->getParamValue("workingDirRelativePath");

my $workflowDataDir = $self->getWorkflowDataDir();

Expand All @@ -26,13 +27,15 @@ sub run {
if ($undo) {
$self->runCmd(0, "rm $workflowDataDir/$nextflowConfigFile");
} else {
my $genomicSequenceFileInNextflowWorkingDirOnCluster = $self->relativePathToNextflowClusterPath($workingDirRelativePath, $genomicSequenceFile);
my $resultsDirectoryInNextflowWorkingDirOnCluster = $self->relativePathToNextflowClusterPath($workingDirRelativePath, $resultsDirectory);
my $nextflowConfig = "$workflowDataDir/$nextflowConfigFile";
open(F, ">$nextflowConfig") || die "Can't open task prop file '$nextflowConfig' for writing";

my $configString = <<NEXTFLOW;
params {
inputFilePath = "$clusterWorkflowDataDir/$genomicSequenceFile"
outputDir = "$clusterWorkflowDataDir/$resultsDirectory"
inputFilePath = $genomicSequenceFileInNextflowWorkingDirOnCluster
outputDir = $resultsDirectoryInNextflowWorkingDirOnCluster
outputFile = "$trnascanOutputFileName"
fastaSubsetSize = $fastaSubsetSize
}
Expand Down
7 changes: 5 additions & 2 deletions Main/lib/perl/WorkflowSteps/MakeTmhmmNextflowConfig.pm
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Expand Up @@ -14,6 +14,7 @@ sub run {
my $nextflowConfigFile = $self->getParamValue("nextflowConfigFile");
my $resultsDirectory = $self->getParamValue("resultsDirectory");
my $outputFileName = $self->getParamValue("outputFileName");
my $workingDirRelativePath = $self->getParamValue("workingDirRelativePath");

my $workflowDataDir = $self->getWorkflowDataDir();

Expand All @@ -34,12 +35,14 @@ sub run {
$self->runCmd(0, "rm $workflowDataDir/$nextflowConfigFile");
} else {
my $nextflowConfig = "$workflowDataDir/$nextflowConfigFile";
my $proteinSequenceFileInNextflowWorkingDirOnCluster = $self->relativePathToNextflowClusterPath($workingDirRelativePath, $proteinSequenceFile);
my $resultsDirectoryInNextflowWorkingDirOnCluster = $self->relativePathToNextflowClusterPath($workingDirRelativePath, $resultsDirectory);
open(F, ">$nextflowConfig") || die "Can't open task prop file '$nextflowConfig' for writing";

my $configString = <<NEXTFLOW;
params {
inputFilePath = "$clusterWorkflowDataDir/$proteinSequenceFile"
outputDir = "$clusterWorkflowDataDir/$resultsDirectory"
inputFilePath = "$proteinSequenceFileInNextflowWorkingDirOnCluster"
outputDir = "$resultsDirectoryInNextflowWorkingDirOnCluster"
outputFileName = "$outputFileName"
fastaSubsetSize = $fastaSubsetSize
}
Expand Down
1 change: 0 additions & 1 deletion Main/lib/perl/WorkflowSteps/NextflowResultsCache.pm
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Expand Up @@ -117,7 +117,6 @@ sub hasCacheFile {
sub copyTo {
my ($self, $test, $undo, $cacheDir, $resultsPath) = @_;


if($undo) {} #nothing to see here
else {
if ($test) {
Expand Down
15 changes: 15 additions & 0 deletions Main/lib/perl/WorkflowSteps/WorkflowStep.pm
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Expand Up @@ -341,6 +341,21 @@ sub runSqlFetchOneRowFromOrgDb {
return @output;
}

sub getClusterNextflowWorkingDir {
my ($self, $relativeDataDirPath) = @_;
my $clusterWorkflowDataDir = $self->getClusterWorkflowDataDir();
return $clusterWorkflowDataDir . "/" . $self->uniqueNameForNextflowWorkingDirectory($relativeDataDirPath);
}

sub relativePathToNextflowClusterPath {
my ($self, $relativeDataDirPath, $fileOrDirRelativePath) = @;
my $clusterNextflowWorkingDir = $self->getClusterNextflowWorkingDir($relativeDataDirPath);

# remove the relativeDataDirPath "prefix" from the fileOrDirRelativePath
my $noPrefix = substr($fileOrDirRelativePath, length($relativeDataDirPath) - length($fileOrDirRelativePath));

return $clusterNextflowWorkingDir . "/" . $noPrefix;
}

1;

23 changes: 0 additions & 23 deletions Main/lib/xml/workflow/HtsSNPsExperiment.xml
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Expand Up @@ -34,33 +34,11 @@
<depends name="makeDataDir"/>
</step>

<!-- make an empty final dir, and mirror it to the cluster. the samples will each mirror their own file -->
<!-- to the cluster, so the mirroring can be done in pieces and in parallel -->

<step name="makeFinalDir" stepClass="ReFlow::StepClasses::MakeDataDir">
<paramValue name="dataDir">$$finalDir$$</paramValue>
<depends name="makeExperimentDatasetLoaderDir"/>
</step>

<step name="mirrorToCluster" stepClass="ReFlow::StepClasses::MirrorToComputeCluster" stepLoadTypes="toCluster">
<paramValue name="fileOrDirToMirror">$$dataDir$$</paramValue>
<depends name="makeSamplesOutputDir"/>
</step>

<step name="mirrorExperimentDatasetLoaderDirToCluster" stepClass="ReFlow::StepClasses::MirrorToComputeCluster" stepLoadTypes="toCluster">
<paramValue name="fileOrDirToMirror">$$dataDir$$/$$experimentDatasetName$$</paramValue>
<depends name="makeExperimentDatasetLoaderDir"/>
<depends name="mirrorToCluster"/>
</step>

<!-- load dataset manually so we can mirror the final dir before filling it with the sample files -->

<step name="mirrorFinalDirToCluster" stepClass="ReFlow::StepClasses::MirrorToComputeCluster" stepLoadTypes="toCluster">
<paramValue name="fileOrDirToMirror">$$finalDir$$</paramValue>
<depends name="makeFinalDir"/>
<depends name="mirrorExperimentDatasetLoaderDirToCluster"/>
</step>

<step name="insertDataset" stepClass="ApiCommonWorkflow::Main::WorkflowSteps::DatasetLoaderInsertDataset">
<paramValue name="datasetName">$$experimentDatasetName$$</paramValue>
<paramValue name="datasetLoaderXmlFileName">$$organismDatasetLoaderXmlFile$$</paramValue>
Expand All @@ -73,7 +51,6 @@
<paramValue name="datasetName">$$experimentDatasetName$$</paramValue>
<paramValue name="datasetLoaderXmlFileName">$$organismDatasetLoaderXmlFile$$</paramValue>
<paramValue name="dataDir">$$dataDir$$/$$experimentDatasetName$$</paramValue>
<depends name="mirrorFinalDirToCluster"/>
</step>

<step name="insertExtDb" stepClass="ApiCommonWorkflow::Main::WorkflowSteps::DatasetLoaderInsertExtDb" stepLoadTypes="plugin">
Expand Down
6 changes: 0 additions & 6 deletions Main/lib/xml/workflow/OrganismSpecific.xml
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Expand Up @@ -21,11 +21,6 @@
<paramValue name="dataDir">$$dataDir$$</paramValue>
</step>

<step name="mirrorToCluster" stepClass="ReFlow::StepClasses::MirrorToComputeCluster" stepLoadTypes="toCluster">
<paramValue name="fileOrDirToMirror">$$dataDir$$</paramValue>
<depends name="makeDataDir"/>
</step>

<subgraph name="genericProfiles" xmlFile="generated/$$projectName$$/$$organismAbbrev$$/genericProfile.xml" excludeIfXmlFileDoesNotExist="true">
<paramValue name="parentDataDir">$$dataDir$$</paramValue>
<paramValue name="organismDatasetLoaderXmlFile">$$organismDatasetLoaderXmlFile$$</paramValue>
Expand Down Expand Up @@ -59,7 +54,6 @@
<paramValue name="organismAbbrev">$$organismAbbrev$$</paramValue>
<paramValue name="relativeWebServicesDir">$$relativeWebServicesDir$$</paramValue>
<paramValue name="proteinsFile">$$proteinsFile$$</paramValue>
<depends name="mirrorToCluster"/>
</subgraph>


Expand Down
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