Final Update to CentOS 5 Compute Node Availability for Broad-hosted Servers

Posted on Wednesday, July 18, 2018 at 03:01PM by Barbara Hill

On June 22, 2018, there was a fire at the main data center for the Broad Institute, resulting in an end of service for the last remaining CentOS 5 node, which enabled the running of the following legacy modules on our Broad-hosted servers:

  • ApplyGatingML
  • CopyNumberInferencePipeline (SNPFileCreator_SNP6, Birdseed, CopyNumberInference, CopyNumberNoise, RemoveCopyNumberOutliers, TangentNormalization, ParallelCBS, SegmentationCount)
  • ESPPredictor
  • FCMSinglePanelQC
  • FLAMEChooseOptimalClusterNumber
  • FLAMEMetacluster
  • FLAMEMixtureModel
  • FlowMeansCluster
  • FlowMergeCluster
  • GLAD
  • IlluminaDASLPipeline (IlluminaScanExtractor, IlluminaNormalizer, IlluminaConcatenate)
  • IlluminaNormalizer
  • ImmPortFCSConvLogicleTrans
  • ImmPort_FLOCK_CrossSample (ImmPortFCSConvLogicleTrans, ImmPortColSelection, ImmPortFLOCK, ImmPortCrossSample)
  • ImmPort_FLOCK_Individual_FCS (ImmPortFCSConvLogicleTrans, ImmPortColSelection, ImmPortFLOCK)
  • MultiplotPreprocess (and thus Multiplot)
  • RemoveCopyNumberOutliers
  • SuggestNumberOfPopulationsFCS
  • TangentNormalization

This means that these modules and pipelines are no longer installed on any of our servers, and the latest versions will be transitioned to the GParc repository, and potentially GitHub (depending on licensing) for archiving.

We are aware that ESPPredictor is a popular module in wide use and will be looking into an updated implementation in the coming months, to be made available, initially, on our Amazon cloud-hosted server, We will post updates as that becomes available.

Please contact us if you have any questions.

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